DART code distributions

u · DART_LAB

+cd models/gitm/GITM2
+./Config.pl -install -compiler=ifortmpif90 -earth
+make
+cd ../work
+./clean.sh 1 1 0 150.0 170.0 1.0 
+
+&dart_to_gitm_nml
+   dart_to_gitm_output_file = 'dart_restart',
+   advance_time_present     = .false.
+   /
+
+&model_nml
+   gitm_restart_dirname         = 'advance_temp_e1/UA/restartOUT',
+   assimilation_period_days     = 0,
+   assimilation_period_seconds  = 1800,
+   model_perturbation_amplitude = 0.2,
+   output_state_vector          = .false.,
+   calendar                     = 'Gregorian',
+   debug                        = 0,
+   gitm_state_variables = 'Temperature',            'KIND_TEMPERATURE',
+                          'eTemperature',           'KIND_TEMPERATURE_ELECTRON',
+                          'ITemperature',           'KIND_TEMPERATURE_ION',
+                          'iO_3P_NDensityS',        'KIND_DENSITY_NEUTRAL_O3P',
+   ...
+
+obs_def/obs_def_upper_atm_mod.f90
+assim_model/assim_model_mod.f90
+common/types_mod.f90
+location/threed_sphere/location_mod.f90
+models/gitm/GITM2/src/ModConstants.f90
+models/gitm/GITM2/src/ModEarth.f90
+models/gitm/GITM2/src/ModKind.f90
+models/gitm/GITM2/src/ModSize.f90
+models/gitm/GITM2/src/ModTime.f90
+models/gitm/GITM2/src/time_routines.f90
+models/gitm/dart_gitm_mod.f90
+models/gitm/dart_to_gitm.f90
+models/gitm/model_mod.f90
+mpi_utilities/null_mpi_utilities_mod.f90
+obs_kind/obs_kind_mod.f90
+random_seq/random_seq_mod.f90
+time_manager/time_manager_mod.f90
+utilities/utilities_mod.f90
+
+cd models/gitm/GITM2
+./Config.pl -install -compiler=ifortmpif90 -earth
+make
+cd ../work
+./clean.sh 1 1 0 150.0 170.0 1.0 
+
+&gitm_to_dart_nml
+   gitm_to_dart_output_file = 'dart_ics',
+   /
+
+&model_nml
+   gitm_restart_dirname         = 'advance_temp_e1/UA/restartOUT',
+   assimilation_period_days     = 0,
+   assimilation_period_seconds  = 1800,
+   model_perturbation_amplitude = 0.2,
+   output_state_vector          = .false.,
+   calendar                     = 'Gregorian',
+   debug                        = 0,
+   gitm_state_variables = 'Temperature',            'KIND_TEMPERATURE',
+                          'eTemperature',           'KIND_TEMPERATURE_ELECTRON',
+                          'ITemperature',           'KIND_TEMPERATURE_ION',
+                          'iO_3P_NDensityS',        'KIND_DENSITY_NEUTRAL_O3P',
+   ...
+
+obs_def/obs_def_upper_atm_mod.f90
+assim_model/assim_model_mod.f90
+common/types_mod.f90
+location/threed_sphere/location_mod.f90
+models/gitm/GITM2/src/ModConstants.f90
+models/gitm/GITM2/src/ModEarth.f90
+models/gitm/GITM2/src/ModKind.f90
+models/gitm/GITM2/src/ModSize.f90
+models/gitm/GITM2/src/ModTime.f90
+models/gitm/GITM2/src/time_routines.f90
+models/gitm/dart_gitm_mod.f90
+models/gitm/gitm_to_dart.f90
+models/gitm/model_mod.f90
+mpi_utilities/null_mpi_utilities_mod.f90
+obs_kind/obs_kind_mod.f90
+random_seq/random_seq_mod.f90
+time_manager/time_manager_mod.f90
+utilities/utilities_mod.f90
+
&mpas_vars_nml
-   mpas_state_variables = 'uReconstructZonal',      'KIND_U_WIND_COMPONENT',
-                          'uReconstructMeridional', 'KIND_V_WIND_COMPONENT',
-                          'w',                      'KIND_VERTICAL_VELOCITY',
-                          'theta',                  'KIND_POTENTIAL_TEMPERATURE',
-                          'qv',                     'KIND_VAPOR_MIXING_RATIO',
-                          'qc',                     'KIND_CLOUDWATER_MIXING_RATIO',
-                          'qr',                     'KIND_RAINWATER_MIXING_RATIO',
-                          'qi',                     'KIND_ICE_MIXING_RATIO',
-                          'qs',                     'KIND_SNOW_MIXING_RATIO',
-                          'qg',                     'KIND_GRAUPEL_MIXING_RATIO',
-                          'surface_pressure',       'KIND_SURFACE_PRESSURE'
-   /
+
+
+The wind options during a DART assimilation
+are controlled by combinations of 4 different namelist options.
+The options control how the forward operators compute expected observation values;
+how the horizontal interpolation is computed; and how the assimilation increments
+are applied to update the wind quantities in the state vector.  Preliminary
+experimental results indicate that using the zonal and meridional winds
+for the forward operator fields and using Barycentric interpolation leads
+to the smoothest estimates of wind quantities, and using increments to update
+the u field gives the least noisy increments.  However there remains
+scientific questions about how best to handle the wind fields under different
+situations.  Thus we have kept all implemented options available for use in
+experimental comparisons.  See the figure below for a flow-chart representation
+of how the 4 namelist items interact:
+
+
+
+Cycling of MPAS/DART is run in a restart mode.
+As for all DART experiments, the overall design for an experiment is this:
+the DART program filter will read the initial
+condition file, the observation sequence file, and the DART namelist
+to decide whether or not to advance the MPAS-ATM model. All of the
+control of the execution of the MPAS model is done by DART directly.
+If the model needs to be advanced, filter makes
+a call to the shell to execute the script
+advance_model.csh,
+which is ENTIRELY responsible
+for getting all the input files, data files, namelists, etc. into
+a temporary directory, running the model, and copying the results
+back to the parent directory (which we call CENTRALDIR).
+The whole process hinges on setting the MPAS-ATM model namelist values
+such that it is doing a restart for every model advance.
+Unlike MPAS-ATM free forecast runs, the forecast step in MPAS/DART requires to 
+set up one more namelist parameter called "config_do_DAcycling = .true." in &restart section 
+of namelist.input to recouple the state vectors (updated by filter) with the mass field for the restart mode.
+For more information, check the advance_model.csh script. 
+
+
+Since DART is an ensemble algorithm, there are multiple analysis files for a single analysis time: 
+one for each ensemble member. Because MPAS/DART is run in a restart mode, each member should keep its own
+MPAS restart file from the previous cycle (rather than having a single template file in CENTRALDIR).
+Creating the initial ensemble of states is an area of active research.
+
+
+
+
+
+
+
[top]

+NAMELIST
+
+This namelist is read from the file input.nml.
+Namelists start with an ampersand
+'&' and terminate with a slash '/'.
+Character strings that contain a '/' must be
+enclosed in quotes to prevent them from
+prematurely terminating the namelist.
+
+
+
++&model_nml
+   model_analysis_filename      = 'mpas_init.nc',
+   grid_definition_filename     = 'mpas_init.nc',
+   output_state_vector          = .false.,
+   vert_localization_coord      = 3,
+   assimilation_period_days     = 0,
+   assimilation_period_seconds  = 21600,
+   model_perturbation_amplitude = 0.0001,
+   log_p_vert_interp            = .true.,
+   calendar                     = 'Gregorian',
+   use_u_for_wind               = .false.,
+   use_rbf_option               = 2,
+   update_u_from_reconstruct    = .true.,
+   use_increments_for_u_update  = .true.,
+   highest_obs_pressure_mb      = 100.0,
+   sfc_elev_max_diff            = -1.0,
+   debug                        = 0,
+/
 
+
 
-These variables are then adjusted to be consistent with observations and 
-   stuffed back into the same netCDF analysis files.  Since DART is an ensemble 
-   algorithm, there are multiple analysis files for a single analysis time: 
-   one for each ensemble member. Creating the initial ensemble of states is an 
-   area of active research.
-   

-   

-   DART reads grid information from the MPAS ATM 'history' file, I have tried to keep
-   the variable names the same. Internal to the DART code, the following variables exist:
+

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+ Item  Type  Description  
model_analysis_filename character(len=256)

+        [default: 'mpas_init.nc'] The name of the MPAS analysis file to be read and/or written 
+        by the DART programs for the state data.
grid_definition_filename character(len=256)

+        [default: 'mpas_init.nc'] The name of the MPAS file to be read 
+        by the DART programs for the grid information.  Generally
+        this is the same as the model_analysis_filename.
+        However, the grid information is large and if the grid is static
+        that information could be omitted from the analysis files to
+        save space. A single grid file could be supplied once and
+        not change during the assimilation run. 
highest_obs_pressure_mb real(r8)

+        [default: 100.0] Observations higher than this pressure are ignored. Set to -1.0
+        to ignore this test.  For models with a prescribed top boundary
+        layer, trying to assimilate very high observations results in 
+        problems because the model damps out any changes the assimilation
+        tries to make.  With adaptive algorithms this results in larger
+        and larger coefficients as the assimilation tries to effect state
+        vector change.
+    
output_state_vector logical [default: .false.] The switch to determine the form of the state vector in the
+        output netCDF files. If .true. 
+        the state vector will be output exactly as DART uses it;
+        as one long array.  If .false., 
+        the state vector is parsed into prognostic variables and 
+        output that way -- much easier to use with 'ncview', for
+        example. [Recommended] 
assimilation_period_days integer [default: 0] The number of days to advance the model for each assimilation.
+        Even if the model is being advanced outside of the DART filter
+        program, the assimilation period should be set correctly. 
+        Only observations with a time within +/- 1/2 this window size 
+        will be assimilated.
+    
assimilation_period_seconds integer [default: 21600] In addition to assimilation_period_days, 
+        the number of seconds to advance the model for each assimilation. 
vert_localization_coord integer [default: 3] Vertical coordinate for vertical localization. 
+       
+          1 = model level
+          2 = pressure (in pascals)
+          3 = height (in meters)
+          4 = scale height (unitless)
+       
sfc_elev_max_diff real(r8)[default: -1.0] If > 0, the maximum difference, in meters, between an observation marked
+        as a 'surface obs' as the vertical type (with the surface elevation, in
+        meters, as the numerical vertical location), and the surface elevation as
+        defined by the model. Observations further away from the surface than this
+        threshold are rejected and not assimilated. If the value is negative, this
+        test is skipped.  
log_p_vert_interp logical [default: .true.] If .true., vertical interpolation is done in log-pressure. Otherwise, linear.
use_u_for_wind logical [default: .false.] If .false., zonal and meridional winds at cell centers are used for 
+        the wind observation operator [default]. In that case, triangular meshes are used for the 
+        barycentric (e.g., area-weighted) interpolation. If .true., wind vectors at an arbitrary
+        (e.g., observation) point are reconstructed from the normal component of velocity on cell edges
+        (u) using radial basis functions (RBFs) provided by the MPAS model.
use_rbf_option integer [default: 2] If use_u_for_wind is .true., this option controls
+        how many points will be used in the RBF interpolation. Options are available as 1, 2, and 3.
+        All the edges available in N (= 1,2, or 3) cells go into the RBF reconstruction. 
update_u_from_reconstruct logical [default: .true.] When zonal and meridional winds at cell centers are used for 
+        the wind observation operator (use_u_for_wind = .false.), 
+        this option decides if the normal component of velocity on cell edges (which is
+        the only wind prognostic variable in MPAS-ATM) should be updated from the winds at cell centers.
+        If .true., use_increments_for_u_update should be also decided. 
+        If use_u_for_wind = .true. and the normal component of velocity on cell
+        edges is defined as a state vector, this option should be .false. so the edge winds can be
+        directly updated by filter. 
use_increments_for_u_update logical [default: .true.] Only if update_u_from_reconstruct is .true., this option is
+        used to decide if the edge winds are replaced by averaging from the analysis
+        winds at cell centers (.false.), or just updated by the analysis increments
+        at cell centers (.true.).  If .true., all the wind components (e.g., both at
+        cell centers and edges) are read from prior and used to compute the
+        increments [Recommended].  
model_perturbation_amplitude real(r8) [default: 0.0001] The amplitude of random noise to add when trying to perturb a single
+        state vector to create an ensemble. Only used when 
+  input.nml::&filter_nml:start_from_restart = .false.
+        
+        Multiplied by the state vector, it produces standard deviation 
+        of a gaussian distribution with the mean at the value of the state vector element. 
calendar character(len=32) 
 
+        [default: 'Gregorian']  Character string specifying the calendar being used by MPAS.
debug integer [default: 0] The switch to specify the run-time verbosity.
+         0 is as quiet as it gets.
+         > 1 provides more run-time messages.
+         > 5 provides ALL run-time messages.  
+    
+
+
+

+

+
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+
+
+
+This namelist contains the list of MPAS variables that make up the DART state vector.
+The order the items are specified controls the order of the data in the
+state vector, so it should not be changed without regenerating any
+DART initial condition or restart files.
+These variables are directly updated by the assimilation in filter.
+Any variables whose values cannot exceed a given
+minimum or maximum can be listed in mpas_state_bounds,
+and when the data is converted back into the MPAS NetCDF files, values
+outside the allowed range will be detected.  Data inside the DART
+state vector and data written to the diagnostic files
+may exceed the allowed limits.
 
 
+
++&mpas_vars_nml
+   mpas_state_variables = 'theta',                 'KIND_POTENTIAL_TEMPERATURE',
+                          'uReconstructZonal',     'KIND_U_WIND_COMPONENT',
+                          'uReconstructMeridional','KIND_V_WIND_COMPONENT',
+                          'qv',                    'KIND_VAPOR_MIXING_RATIO',
+                          'qc',                    'KIND_CLOUDWATER_MIXING_RATIO',
+                          'surface_pressure',      'KIND_SURFACE_PRESSURE'
+   mpas_state_bounds    = 'qv','0.0','NULL','CLAMP',
+                          'qc','0.0','NULL','CLAMP',
+/
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+ Item  Type  Description  
mpas_vars_nml character(len=NF90_MAX_NAME)::

+                   dimension(160)
+    The table that relates the MPAS-ATM variables 
+        to use to build the DART state vector, and the corresponding 
+        DART kinds for those variables.  The first column in each pair must
+        be the NetCDF name of a field in the MPAS file.  The second column
+        in each pair must be a KIND known to the DART system.  See the
+        obs_kind/obs_kind_mod.f90 file for known names.
+        These must be generic kinds, not specific types.
+    
mpas_state_bounds character(len=NF90_MAX_NAME)::

+                   dimension(160)
+     MPAS-ATM variables that need to set up lower and upper bound values.
+         Columns are a variable name, min, max values, and 'CLAMP' or 'FAIL' in case
+         the field goes beyond the bounds. If the bound values have 'NULL', 
+         the actual data range is used.
+
+
+

+

+
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+
+[top]

+Grid information
+As the forward operators use the unstructured grid meshes in MPAS-ATM, the DART/MPAS interface needs to read static 
+   variables related to the grid structure from the MPAS ATM 'history' file (specified in 
+   model_analysis_filename). 
+   These variables are used to find the closest cell to an observation 
+   point in the cartesian coordinate (to avoid the polar issues). 
+
+
 
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+integer :: nCells        the number of Cell Centers
integer :: nEdges        the number of Cell Edges 
integer :: nVertices     the number of Cell Vertices
integer :: nVertLevels   the number of vertical level midpoints
integer :: nVertLevelsP1 the number of vertical level edges
integer :: nSoilLevels   the number of soil level ?midpoints?
real(r8) :: latCell(:)   the latitudes  of the Cell Centers (-90,90) 
real(r8) :: lonCell(:)   the longitudes of the Cell Centers [0, 360) 
real(r8) :: zgrid(:,:)   cell center geometric height at cell centers (ncells,nvert) 
integer :: nCells        the number of cell centers
integer :: nEdges        the number of cell edges 
integer :: nVertices     the number of cell vertices
integer :: nVertLevels   the number of vertical levels for mass fields
integer :: nVertLevelsP1 the number of vertical levels for vertical velocity
integer :: nSoilLevels   the number of soil levels
real(r8) :: latCell(:)   the latitudes  of the cell centers [-90,90] 
real(r8) :: lonCell(:)   the longitudes of the cell centers [0, 360] 
real(r8) :: latEdge(:)   the latitudes  of the edges [-90,90], if edge winds are used. 
real(r8) :: lonEdge(:)   the longitudes of the edges [0, 360], if edge winds are used. 
real(r8) :: xVertex(:)   The cartesian location in x-axis of the vertex 
real(r8) :: yVertex(:)   The cartesian location in y-axis of the vertex 
real(r8) :: zVertex(:)   The cartesian location in z-axis of the vertex 
real(r8) :: xEdge(:)   The cartesian location in x-axis of the edge, if edge winds are used. 
real(r8) :: yEdge(:)   The cartesian location in y-axis of the edge, if edge winds are used. 
real(r8) :: zEdge(:)   The cartesian location in z-axis of the edge, if edge winds are used. 
real(r8) :: zgrid(:,:)   geometric height at cell centers (nCells, nVertLevelsP1)
 integer  :: CellsOnVertex(:,:)   list of cell centers defining a triangle 
integer  :: edgesOnCell(:,:)   list of edges on each cell 
integer  :: verticesOnCell(:,:)   list of vertices on each cell 
integer  :: edgeNormalVectors(:,:)   unit direction vectors on the edges (only used if use_u_for_wind = .true.)
 
+

 
-   model_mod variable storage
+
+
+[top]

+model_mod variable storage
 
    
-   input.nml&mpas_vars_nml 
+   input.nml :: &mpas_vars_nml 
    defines the list of MPAS variables used to build the DART state vector. 
    Combined with an MPAS analysis file, the information is used to 
    determine the size of the DART state vector and derive the metadata.
@@ -109,17 +437,19 @@
    character(len=NF90_MAX_NAME), dimension(NF90_MAX_VAR_DIMS) :: dimname
    integer, dimension(NF90_MAX_VAR_DIMS) :: dimlens
    integer :: xtype         ! netCDF variable type (NF90_double, etc.) 
-   integer :: numdims       ! number of dims - excluding TIME
+   integer :: numdims       ! number of dimensions - excluding TIME
    integer :: numvertical   ! number of vertical levels in variable
-   integer :: numcells      ! number of horizontal locations (typically cell centers)
-   logical :: ZonHalf       ! vertical coordinate has dimension nVertLevels
-   integer :: varsize       ! prod(dimlens(1:numdims))
+   integer :: numcells      ! number of cell locations (typically cell centers)
+   integer :: numedges      ! number of edge locations (edges for normal velocity)
+   logical :: ZonHalf       ! vertical coordinate for mass fields (nVertLevels)
+   integer :: varsize       ! variable size (dimlens(1:numdims))
    integer :: index1        ! location in dart state vector of first occurrence
    integer :: indexN        ! location in dart state vector of last  occurrence
    integer :: dart_kind
    character(len=paramname_length) :: kind_string
    logical  :: clamping     ! does variable need to be range-restricted before 
-   real(r8) :: range(2)     ! being stuffed back into MPAS analysis file.
+   real(r8) :: range(2)     ! lower and upper bounds for the data range.
+   logical  :: out_of_range_fail  ! is out of range fatal if range-checking?
 end type progvartype
 
 type(progvartype), dimension(max_state_variables) :: progvar
@@ -134,28 +464,36 @@
    x(nVertical,nHorizontal,nVariables). The fastest-varying dimension is vertical,
    then horizontal, then variable ... naturally, the DART state vector is 1D. 
    Each variable is also stored this way in the MPAS analysis file.
+   

    
 
-
-   The DART interface for MPAS (atm)
-   
-      was compiled with the gfortran 4.2.3 compilers and run on a Mac.
-      

-      

-      The DART components were built with the following mkmf.template settings:
-   
-   -      FC = gfortran
-      LD = gfortran
-      NETCDF = /Users/thoar/GNU
-      INCS = -I${NETCDF}/include
-      LIBS = -L${NETCDF}/lib -lnetcdf -lcurl -lhdf5_hl -lhdf5 -lz  -lm
-      FFLAGS = -O0 -fbounds-check -frecord-marker=4 -ffpe-trap=invalid $(INCS)
-      LDFLAGS = $(FFLAGS) $(LIBS)
-   
- 
+

+
+
+[top]

+Compilation
 
+
+The DART interface for MPAS-ATM can be compiled with various fortran compilers such as (but not limited to) 
+gfortran, pgf90, and intel. It has been tested on a Mac and NCAR IBM supercomputer (yellowstone).
+
+
+
+NOTE: While MPAS requires the PIO (Parallel IO) and pNetCDF
+(Parallel NetCDF) libraries, DART uses only the plain NetCDF libraries.
+If an altered NetCDF library is required by the parallel versions, there may 
+be incompatibilities between the run-time requirements of DART and MPAS.
+Static linking of one or the other executable, or swapping of modules
+between executions may be necessary.
+
+
+

+
+
 
+[top]

+Conversions
+
 
    Converting between DART files and MPAS analysis files
    is relatively straightforward. Given the namelist mechanism for
@@ -173,7 +511,7 @@
    
    
-       
@@ -188,7 +526,7 @@
        dart_to_model updates the MPAS analysis file 
        specified in input.nmlmodel_nml:model_analysis_filename.
        If the DART file contains an 'advance_to' time, separate control information is written 
-       to an auxiliary file that is used by the advance_model.csh script.
+       to an auxiliary file (named 'mpas_time') that is used by the advance_model.csh script.
        
    model_to_dart.f90 converts an MPAS analysis file (nominally named mpas_analysis.nc) into a 
+       converts an MPAS analysis file (nominally named mpas_init.nc) into a 
        DART-compatible file normally called dart_ics .
        We usually wind up linking the actual analysis file to a static name that is used by DART.
        
    
    
@@ -212,53 +550,59 @@
 
 
 
-366 mirage2:thoar% ncdump -h mpas_analysis.nc
+366 mirage2:thoar% ncdump -h mpas_init.nc
 netcdf mpas_analysis {
 dimensions:
         StrLen = 64 ;
         Time = UNLIMITED ; // (1 currently)
-        nCells = 10242 ;                                  available in DART
-        nEdges = 30720 ;                                  available in DART
+        nCells = 10242 ;                                  available in DART
+        nEdges = 30720 ;                                  available in DART
         maxEdges = 10 ;
         maxEdges2 = 20 ;
-        nVertices = 20480 ;                               available in DART
+        nVertices = 20480 ;                               available in DART
         TWO = 2 ;
         THREE = 3 ;
-        vertexDegree = 3 ;                                available in DART
+        vertexDegree = 3 ;
         FIFTEEN = 15 ;
         TWENTYONE = 21 ;
         R3 = 3 ;
-        nVertLevels = 41 ;                                available in DART
-        nVertLevelsP1 = 42 ;                              available in DART
+        nVertLevels = 41 ;                                available in DART
+        nVertLevelsP1 = 42 ;                              available in DART
         nMonths = 12 ;
         nVertLevelsP2 = 43 ;
-        nSoilLevels = 4 ;                                 available in DART
+        nSoilLevels = 4 ;                                 available in DART
 variables:
-        char xtime(Time, StrLen) ;                        available in DART
-        double latCell(nCells) ;                          available in DART
-        double lonCell(nCells) ;                          available in DART
-        double latEdge(nEdges) ;
-        double lonEdge(nEdges) ;
+        char xtime(Time, StrLen) ;                        available in DART
+        double latCell(nCells) ;                          available in DART
+        double lonCell(nCells) ;                          available in DART
+        double latEdge(nEdges) ;                          available in DART
+        double lonEdge(nEdges) ;                          available in DART
         int indexToEdgeID(nEdges) ;
         double latVertex(nVertices) ;
         double lonVertex(nVertices) ;
+	double xVertex(nVertices) ;                       available in DART
+	double yVertex(nVertices) ;                       available in DART
+	double zVertex(nVertices) ;                       available in DART
+	double xEdge(nVertices) ;                         available in DART
+	double yEdge(nVertices) ;                         available in DART
+	double zEdge(nVertices) ;                         available in DART
         int indexToVertexID(nVertices) ;
         int cellsOnEdge(nEdges, TWO) ;
         int nEdgesOnCell(nCells) ;
         int nEdgesOnEdge(nEdges) ;
-        int edgesOnCell(nCells, maxEdges) ;
+        int edgesOnCell(nCells, maxEdges) ;               available in DART
         int edgesOnEdge(nEdges, maxEdges2) ;
         double weightsOnEdge(nEdges, maxEdges2) ;
         double dvEdge(nEdges) ;
         double dcEdge(nEdges) ;
         double angleEdge(nEdges) ;
-        double edgeNormalVectors(nEdges, R3) ;
+        double edgeNormalVectors(nEdges, R3) ;            available in DART
         double cellTangentPlane(nEdges, TWO, R3) ;
         int cellsOnCell(nCells, maxEdges) ;
-        int verticesOnCell(nCells, maxEdges) ;
+        int verticesOnCell(nCells, maxEdges) ;            available in DART
         int verticesOnEdge(nEdges, TWO) ;
         int edgesOnVertex(nVertices, vertexDegree) ;
-        int cellsOnVertex(nVertices, vertexDegree) ;      available in DART
+        int cellsOnVertex(nVertices, vertexDegree) ;      available in DART
         double kiteAreasOnVertex(nVertices, vertexDegree) ;
         double rainc(Time, nCells) ;
         double cuprec(Time, nCells) ;
@@ -327,182 +671,7 @@
 
 
 
-
-
-
 
-
-[top]

-NAMELIST
-We adhere to the F90 standard of starting a namelist with an ampersand
-'&' and terminating with a slash '/' for all our namelist input.
-Consider yourself forewarned that character strings that contain a '/' must be
-enclosed in quotes to prevent them from prematurely terminating the namelist.
-
--namelist /model_nml/  model_analysis_filename, &
-          assimilation_period_days, assimilation_period_seconds, &
-          model_perturbation_amplitude, output_state_vector, calendar, debug
-
-
-
-
-
-
-This namelist is read in a file called input.nml.
-   This namelist provides control over the assimilation period for the model.
-   All observations within (+/-) half of the assimilation period are assimilated.
-   The assimilation period is the minimum amount of time the model can be advanced,
-   and checks are performed to ensure that the assimilation window is a multiple of
-   the model dynamical timestep. This also specifies the MPAS analysis file that will
-   be read and/or written by the different program units.
-
-
-
-
-    
-    
-
-
-    
-    
-
-
-    
-    
-
-
-    
-    
-
-
-    
-    
-
-
-    
-     
-
-
-    
-    
-
-
-    
-    
-
-Contents    Type        Description 
model_analysis_filename character(len=256)

-                  [default: 'mpas_analysis.nc'] Character string specifying the name of the MPAS analysis 
-                       file to be read and/or written by the different program units.
output_state_vector logical [default: .true.] The switch to determine the form of the state vector in the
-                       output netCDF files. If .true. 
-                       the state vector will be output exactly as DART uses it 
-                       ... one long array.  If .false., 
-                       the state vector is parsed into prognostic variables and 
-                       output that way -- much easier to use with 'ncview', for
-                       example.
assimilation_period_days integer [default: 1] The number of days to advance the model for each assimilation.
-                       
assimilation_period_seconds integer [default: 0] In addition to assimilation_period_days, 
-                    the number of seconds to advance the model for each assimilation.
-                       
model_perturbation_amplitude real(r8) [default: 0.2]  Reserved for future use.
-                   
calendar character(len=32) 
 
-                       [default: 'Gregorian'] 
-                       Character string specifying the calendar being used by MPAS.
debug integer [default: 0] The switch to specify the run-time verbosity.
-                       0 is as quiet as it gets.
-                       > 1 provides more run-time messages.
-                       > 5 provides ALL run-time messages.
-                       
-
-Example
-
--&model_nml
-   model_analysis_filename      = 'mpas_restart.nc';
-   assimilation_period_days     = 0,
-   assimilation_period_seconds  = 60,
-   model_perturbation_amplitude = 0.2,
-   output_state_vector          = .true.,
-   calendar                     = 'Gregorian',
-   debug                        = 0
-   /
-
-
-
-

-
-
-
-
-

--namelist /mpas_vars_nml/ mpas_state_variables
-
-
-
-
-
-
-

@@ Diff output truncated at 40000 characters. @@

From nancy at ucar.edu  Wed Dec 11 08:36:50 2013
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Wed, 11 Dec 2013 08:36:50 -0700
Subject: [Dart-dev] [6668] DART/trunk/models/mpas_atm/model_mod.html: a few
 addition changes suggested by soyoung, a typo fix, 
Message-ID: 

Revision: 6668
Author:   nancy
Date:     2013-12-11 08:36:48 -0700 (Wed, 11 Dec 2013)
Log Message:
-----------
a few addition changes suggested by soyoung, a typo fix,
and then more futzing by me on some wordsmithing.

Modified Paths:
--------------
    DART/trunk/models/mpas_atm/model_mod.html

-------------- next part --------------
Modified: DART/trunk/models/mpas_atm/model_mod.html
===================================================================

--- DART/trunk/models/mpas_atm/model_mod.html	2013-12-10 23:54:28 UTC (rev 6667)
+++ DART/trunk/models/mpas_atm/model_mod.html	2013-12-11 15:36:48 UTC (rev 6668)
@@ -53,14 +53,17 @@
 
 

 The wind options during a DART assimilation
-are controlled by combinations of 4 different namelist options.
-The options control how the forward operators compute expected observation values;
-how the horizontal interpolation is computed; and how the assimilation increments
-are applied to update the wind quantities in the state vector.  Preliminary
-experimental results indicate that using the zonal and meridional winds
-for the forward operator fields and using Barycentric interpolation leads
-to the smoothest estimates of wind quantities, and using increments to update
-the u field gives the least noisy increments.  However there remains
+are controlled by combinations of 4 different namelist values.
+The values determine which fields the forward operator uses to compute expected 
+observation values; how the horizontal interpolation is computed in that
+forward operator; and how the assimilation increments
+are applied to update the wind quantities in the state vector.
+Preliminary results based on real data assimilation experiments indicate that 
+performance is better when the zonal and meridional winds are used as
+input to the forward operator that uses Barycentric interpolation, and when the 
+prognostic u wind is updated by the incremental method described in
+the figure below.
+However there remain
 scientific questions about how best to handle the wind fields under different
 situations.  Thus we have kept all implemented options available for use in
 experimental comparisons.  See the figure below for a flow-chart representation
@@ -305,17 +308,27 @@
 
 
 

-This namelist contains the list of MPAS variables that make up the DART state vector.
+The &mpas_vars_nml namelist contains the list 
+of MPAS variables that make up the DART state vector.
 The order the items are specified controls the order of the data in the
-state vector, so it should not be changed without regenerating any
+state vector, so it should not be changed without regenerating all
 DART initial condition or restart files.
-These variables are directly updated by the assimilation in filter.
+These variables are directly updated by the filter assimilation.
+
+
 Any variables whose values cannot exceed a given
-minimum or maximum can be listed in mpas_state_bounds,
-and when the data is converted back into the MPAS NetCDF files, values
-outside the allowed range will be detected.  Data inside the DART
-state vector and data written to the diagnostic files
-may exceed the allowed limits.
+minimum or maximum can be listed in mpas_state_bounds.
+When the data is written back into the MPAS NetCDF files values
+outside the allowed range will be detected and changed.  
+Data inside the DART state vector and data written to 
+the DART diagnostic files will not go through this test and
+values may exceed the allowed limits.
+Note that changing values at the edges of the distribution
+means it is no longer completely gaussian.  In practice
+this technique has worked effectively, but if the assimilation
+is continually trying to move the values outside the permitted
+range the results may be of poor quality.  Examine the diagnostics for
+these fields carefully when using bounds to restrict their values.
 
 
 
@@ -349,23 +362,29 @@
 mpas_vars_nml
     character(len=NF90_MAX_NAME)::

                    dimension(160)
-    The table that relates the MPAS-ATM variables 
-        to use to build the DART state vector, and the corresponding 
-        DART kinds for those variables.  The first column in each pair must
-        be the NetCDF name of a field in the MPAS file.  The second column
-        in each pair must be a KIND known to the DART system.  See the
-        obs_kind/obs_kind_mod.f90 file for known names.
-        These must be generic kinds, not specific types.
+    The table that both specifies which MPAS-ATM variables will be
+        placed in the state vector, and also relates those variables 
+        to the corresponding DART kinds.  The first column in each pair must
+        be the exact NetCDF name of a field in the MPAS file.  The second column
+        in each pair must be a KIND known to the DART system.  See 
+        obs_kind/obs_kind_mod.f90 for known names.
+        This file is autogenerated when DART builds filter for a particular
+        model, so run quickbuild.csh in the work directory
+        first before examining this file.  Use the generic kind list in 
+        the obs_kind_mod tables, not the specific type list.
     
 
 
 mpas_state_bounds
     character(len=NF90_MAX_NAME)::

                    dimension(160)
-     MPAS-ATM variables that need to set up lower and upper bound values.
-         Columns are a variable name, min, max values, and 'CLAMP' or 'FAIL' in case
-         the field goes beyond the bounds. If the bound values have 'NULL', 
-         the actual data range is used.
+     List only MPAS-ATM variables that must restrict their values to remain
+         between given lower and/or upper bounds.
+         Columns are: NetCDF variable name, min value, max value, and action to take
+         for out-of-range values.  Either min or max can have the string 'NULL' to indicate
+         no limiting will be done.  If the action is 'CLAMP' out of range values will be
+         changed to the corresponding bound and execution continues; 
+         'FAIL' stops the executable if out of range values are detected.
 
 
 
@@ -1439,7 +1458,7 @@
 [top]

 REFERENCES
 
- The Data Assimilation section in the MPAS documentatino
+
 The Data Assimilation section in the MPAS documentation
 found at  
 http://mpas-dev.github.io
 

From nancy at ucar.edu  Wed Dec 11 13:41:42 2013
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Wed, 11 Dec 2013 13:41:42 -0700
Subject: [Dart-dev] [6671] DART/trunk/doc/html: restore the previous version
 release notes in a 'history' directory
Message-ID: 

Revision: 6671
Author:   nancy
Date:     2013-12-11 13:41:41 -0700 (Wed, 11 Dec 2013)
Log Message:
-----------
restore the previous version release notes in a 'history' directory
so we have a record of the release changes.  move some of the remaining
old release notes into the history dir.  change the links so they are
at the right level - include 'history/' where needed, add '../' to
relative path names.   update the recommended version in index.shtml
and fix the release date.

Modified Paths:
--------------
    DART/trunk/doc/html/index.shtml

Added Paths:
-----------
    DART/trunk/doc/html/history/
    DART/trunk/doc/html/history/ASP_DART_exercise.html
    DART/trunk/doc/html/history/DART_ASP_Summer2003.html
    DART/trunk/doc/html/history/Fiji_release.html
    DART/trunk/doc/html/history/Guam_release.html
    DART/trunk/doc/html/history/I_diffs_from_workshop.html
    DART/trunk/doc/html/history/Iceland_release.html
    DART/trunk/doc/html/history/Jamaica_diffs_from_I.html
    DART/trunk/doc/html/history/Jamaica_release.html
    DART/trunk/doc/html/history/Kodiak_release.html
    DART/trunk/doc/html/history/PostI_diffs_from_I.html
    DART/trunk/doc/html/history/Post_Iceland_release.html
    DART/trunk/doc/html/history/hawaii_release.html
    DART/trunk/doc/html/history/pre_guam_release.html
    DART/trunk/doc/html/history/pre_hawaii_release.html
    DART/trunk/doc/html/history/pre_j_release.html

Removed Paths:
-------------
    DART/trunk/doc/html/ASP_DART_exercise.html
    DART/trunk/doc/html/DART_ASP_Summer2003.html
    DART/trunk/doc/html/Kodiak_release.html

-------------- next part --------------
Deleted: DART/trunk/doc/html/ASP_DART_exercise.html
===================================================================
--- DART/trunk/doc/html/ASP_DART_exercise.html	2013-12-11 19:08:21 UTC (rev 6670)
+++ DART/trunk/doc/html/ASP_DART_exercise.html	2013-12-11 20:41:41 UTC (rev 6671)
@@ -1,1308 +0,0 @@
-
-
-
-ASP Summer Colloquium DART Exercise Documentation
-
-
-
-
-
-
-
-TERMS OF USE
-
-
-
-Document conventions
-Anything underlined is a URL.

-All filenames look like this -- (typewriter font, green).

-Program names look like this -- (italicized font, green).

-user input looks like this -- (bold, magenta).
-
-
-commands to be typed at the command line are contained in an 
-indented gray box.
-
-
-And the contents of a file are enclosed in a box with a border:
-
-
-&hypothetical_nml

-  obs_seq_in_file_name = "obs_seq.in",

-  obs_seq_out_file_name = "obs_seq.out",

-  init_time_days = 0,

-  init_time_seconds = 0,

-  output_interval = 1   /
-
-
-
-
-
-Overview of DART
-$Id$
-
-The Data Assimilation Research Testbed (DART) is designed to 
-facilitate the combination of assimilation algorithms, models, 
-and observation sets to allow increased understanding of all three. 
-(an 
-in-depth design discussion)
-For the 
-ASP colloquium 
-on Data Assimilation, a subset of the complete DART facility was 
-used to examine ensemble filter assimilation algorithms using 
-synthetic observations.  
-The DART programs were compiled with the Intel 7.1 Fortran compiler 
-and run on a linux compute-server while analysis was performed with 
-Matlab on a DEC workstation. If your system is different, you will 
-definitely need to read the 
-Customizations section.
-
-
-DART programs can require three different types of input. 
-First, some of the DART programs, those for creating synthetic
-observational datasets, require interactive input from the keyboard. 
-For simple cases, this interactive input can be made directly 
-from the keyboard. In more complicated cases, a file containing 
-the appropriate keyboard input can be created and this file 
-can be directed to the standard input of the DART program. 
-Second, many DART programs expect one or more input files in 
-DART specific formats to be available. For instance, 
-perfect_model_obs creates a synthetic 
-observation set given a particular model and a description 
-of a sequence of observations requires an input file that 
-describes this observation sequence.
-At present, all DART-specific input files are inefficient but 
-human-readable ascii files. Third, many DART 
-modules (including main programs) make use of the Fortan90 
-namelist facility to obtain values of certain parameters 
-at run-time. All programs look for a namelist input file 
-called input.nml in the directory in which 
-the program is executed. The input.nml 
-file can contain a sequence of individual Fortran90 namelists 
-which specify values of particular parameters for modules that 
-compose the executable program.
-Unfortunately, the Fortran90 namelist interface 
-is poorly defined in the language standard, leaving 
-considerable leeway to compiler developers in implementing the 
-facility. The Intel 7.1 compiler has some particularly unpleasant 
-behavior when a namelist file contains an entry that is NOT defined 
-in the program reading the namelist.
-Error behavior is unpredictable, but often results in read 
-errors for other input files opened by DART programs.
-If you encounter run-time read errors, the first course of action
-should be to ensure the components of the namelist are actual components.
-Changing the names of the namelist components will
-create unpleasantries.
-
-
-
-DART uses the 
-netCDF 
-self-describing data format with a particular metadata convention to 
-describe output that is used to analyze the results of assimilation 
-experiments. These files have the extension .nc 
-and can be read by a number of standard data analysis tools. 
-Three sets of tools are available to work with netCDF files for the ASP 
-colloquium. First, the simple tool ncview is 
-provided to do rudimentary graphical display of slices of output 
-data fields. 
-ncview 
-will be of most use for output of the more comprehensive models at 
-the end of the exercise set. Second, a set of tools called the 
-NCO tools, produced by 
-UCAR's Unidata group, are aailable to do operations like 
-concatenating, slicing, and dicing of netCDF files. 
-Finally, a set of Matlab
-scripts, designed to produce graphical diagnostics from DART netCDF 
-output files are available.
-
-
-
-This document outlines the installation of the DART software
-and the system requirements. For convenience, some of the original 
-colloquium exercises are repeated here, mostly just to check the
-installation. The entire installation process is summarized in
-the following steps:
-
-
-Determine which F90 compiler is available.
-    Determine the location of the 
-        netCDF library.
-    Determine the location of the 
-        udunits library.
-    Download the DART software bundle and untar it 
-        into the expected source tree.
-    Modify certain DART files to reflect 
-        the available F90 compiler and location of the 
-	appropriate libraries.
-    Build the executables.
-
-
-
-We have tried to make the code as portable as possible, but we
-do not have access to all compilers on all platforms, so there are no
-guarantees. We are interested in your experience building the system,
-so please email me (Tim Hoar) at thoar @ ucar . edu
-
-
-
-After the installation, you might want to peruse the following.
-
-
-Running the Lorenz_63 Model.
-    Using the Matlab diagnostic scripts.
-    A short discussion on 
-    bias, filter divergence and covariance inflation.
-    And another one on 
-     synthetic observations.
-
-
-
-
-
-
-Requirements: an F90 Compiler
-
-
-The DART software has been successfully built on several Linux/x86
-platforms with the 
-Intel Fortran
-Compiler 7.1 for Linux, which is free for individual scientific use. 
-It has also been built and successfully run with the 
-Portland Group Fortran Compiler. 
-Since recompiling the code is a necessity to experiment
-with different models, there are no binaries to distribute.
-
-
-
-
-
-
-Requirements: the netCDF library
-
-
-DART uses the 
-netCDF 
-self-describing data format for the results of assimilation 
-experiments. These files have the extension .nc 
-and can be read by a number of standard data analysis tools. 
-In particular, DART also makes use of the F90 interface to the library
-which are available through the netcdf.mod and
-typesizes.mod modules. 
-IMPORTANT: different compilers create these modules with
-different "case" filenames, and sometimes they are not both
-installed into the expected directory. It is required that both modules
-be present. The normal place would be in the netcdf/include 
-directory, as opposed to the  netcdf/lib directory.
-
-
-
-If the netCDF library does not exist on your system, you must build
-it (as well as the F90 interface modules). The library and instructions 
-for building the library or installing from an RPM may be found at 
-the netCDF home page: 
-
-http://www.unidata.ucar.edu/packages/netcdf/ 
-Pay particular attention to the compiler-specific patches that must 
-be applied for the Intel Fortran Compiler. (Or the PG compiler, for
-that matter.)
-
-
-
-The location of the netCDF library, libnetcdf.a,
-and the locations of both netcdf.mod and
-typesizes.mod will be needed by the makefile
-template, as described in the compiling
-section.
-
-
-
-
-
-
-Requirements: the udunits library
-
-DART also uses the very common 
-
-udunits library for manipulating units of physical quantities. If,
-somehow, it is not installed on your system, you will need to install
-it (instructions are available from 
-Unidata's Downloads page).
-
-
-
-The location of the udunits library, libudunits.a,
-will be needed by the makefile template, as described in the 
-compiling section.
-
-
-
-
-
-
-Unpacking the distribution.
-
-
-The DART source code is distributed as a compressed tar file. 
-DART_ASP_SUMMER_2003.tar.gz
-[8307414 bytes]. When untarred, the source tree will begin with a 
-directory named DART and will be approximately 
-23.5Mb. Compiling the code in this tree (as is usually the case) will
-necessitate much more space.
-
-
-
-   gunzip DART_ASP_SUMMER_2003.tar.gz

-   tar -xvf DART_ASP_SUMMER_2003.tar

-
-
-
-The code tree is very "bushy"; there are many directories of support
-routines, etc. but only a few directories involved with the
-customization and installation of the DART software. If you can
-compile and run ONE of the low-order models, you should be able to
-compile and run ANY of the low-order models. For this reason,
-we can focus on the Lorenz `63 model. Subsequently, the only
-directories with files to be modified to check the installation 
-are:
- DART/mkmf,
- DART/models/lorenz_63/work, and 
- DART/matlab (but only for analysis).
-
-
-
-
-
-
-Customizing the build scripts -- Overview.
-
-
-DART executable programs are constructed using two tools: 
-make and 
-mkmf. 
-The make utility is a relatively common
-piece of software that requires a user-defined input file that records 
-dependencies between different source files. make 
-then performs a hierarchy of actions when one or more of the
-source files is modified. The mkmf utility is 
-a custom preprocessor that generates
-a make input file 
-(named Makefile) and is designed specifically to work
-with object-oriented Fortran90 (and other languages) for systems like
-DART.
-
-
-
-mkmf requires two separate input files. 
-The first is a `template' file which specifies details of the commands 
-required for a specific Fortran90 compiler and may also contain 
-pointers to directories containing pre-compiled utilities required by 
-the DART system. This template file will need to 
-be modified to reflect your system. The second input file is a 
-`path_names' file which includes a complete list of the locations 
-(either relative or absolute) of all Fortran90 source files that are 
-required to produce a particular DART program. 
-Each 'path_names' file must contain a path for 
-exactly one Fortran90 file containing a main program, 
-but may contain any number of additional paths pointing to files 
-containing Fortran90 modules. 
-An mkmf command is executed which 
-uses the 'path_names' file and the mkmf template file to produce a 
-Makefile which is subsequently used by the
-standard make utility.
-
-
-
-Shell scripts that execute the mkmf command for all standard 
-DART executables are provided as part of the standard DART software. 
-For more information on mkmf see 
-the FMS mkmf description
-
-
-
-Customizing the 'mkmf.template' file
-
-
-A series of templates for different compilers/architectures exists 
-in the DART/mkmf/ directory and have names with
-extensions that identify either the compiler, the architecture, or both. 
-This is how you inform the build process of the specifics of your system. 
-For the discussion that follows, knowledge of the contents of one of these
-templates (i.e. mkmf.template.pgi) is needed: 
-(note that only the first few lines are shown here)
-
-
-
-# Makefile template for PGI f90

-FC = pgf90

-CPPFLAGS =

-FFLAGS = -r8 -Ktrap=fp -pc 64 -I/usr/local/netcdf/include

-LD = pgf90

-LDFLAGS = $(LIBS)

-LIBS = -L/usr/local/netcdf/lib -lnetcdf -L/usr/local/udunits-1.11.7/lib -ludunits

-LIST = -Mlist

-

-# you should never need to change any lines below.

-...

-
-
-
-Essentially, each of the lines defines some part of the resulting 
-Makefile. Since make
-is particularly good at sorting out dependencies, the order of these 
-lines really doesn't make any difference.
-The FC = pgf90 line ultimately defines the 
-Fortran90 compiler to use, etc.
-The lines which are most likely to need site-specific changes 
-start with FFLAGS and LIBS, which 
-indicate where to look for the netCDF F90 modules and the 
-location of the netCDF and udunits libraries.
-
-
-
-FFLAGS
-
-
-Each compiler has different compile flags, so there is really no way
-to exhaustively cover this other than to say the templates as we supply
-them should work -- depending on the location of the netCDF modules 
-netcdf.mod and
-typesizes.mod.
-Change the /usr/local/netcdf/include string to
-reflect the location of your modules.
-The low-order models can be compiled without the -r8 
-switch, but the bgrid_solo model cannot. 
-
-
-
-LIBS
-
-
-Modifying the LIBS value should be relatively
-straightforward.

-Change the /usr/local/netcdf/lib string to
-reflect the location of your libnetcdf.a.

-Change the /usr/local/udunits-1.11.7/lib string to
-reflect the location of your libudunits.a.
-
-
-
-Customizing the 'path_name' file
-
-
-Several path_name_* files are provided in
-the work directory for each specific model, 
-in this case: DART/models/lorenz_63/work.
-
-
-
-   path_names_create_obs_set_def
-   path_names_create_obs_sequence
-   path_names_perfect_model_obs
-   path_names_filter
-
-
-
-Since each model comes with its own set of files, no customization is
-needed.
-
-
-
-
-
-
-Building the Lorenz_63 DART project.
-
-Currently, DART executables are constructed in a work 
-subdirectory under the directory containing code for the given model.
-In the top-level DART directory, change to the L63 work 
-directory and list the contents:
-
-
-
-cd DART/models/lorenz_63/work

-ls -1
-


-
-With the result:
-filter_ics 
-input.nml 
-mkmf_create_obs_sequence 
-mkmf_create_obs_set_def 
-mkmf_filter 
-mkmf_perfect_model_obs 
-path_names_create_obs_sequence 
-path_names_create_obs_set_def 
-path_names_filter 
-path_names_perfect_model_obs 
-perfect_ics
-
-
-There are four mkmf_xxxxxx 
-files for the programs 
-create_obs_set_def, 
-create_obs_sequence, 
-perfect_model_obs, and 
-filter along with the 
-corresponding path_names_xxxxxx files.
-You can examine the contents of one of the 
-path_names_xxxxxx files, 
-for instance path_names_filter, to see a list of 
-the relative paths of all files that contain Fortran90 modules 
-required for the program filter for 
-the L63 model. All of these paths are relative to the 
-DART directory that you copied into 
-your local storage. The first path is the main program 
-(filter.f90) and is followed by all 
-the Fortran90 modules used by this program.
-
-
-
-The mkmf_xxxxxx scripts 
-are considerably more cryptic and need to be modified to use the appropriate
-DART/mkmf/mkmf.template.xxx 
-file containing the site-specific customizations of the previous section 
-(i.e. the template customization section). 
-For example, suppose you modified 
-DART/mkmf/mkmf.template.ifc 
-and want to create the create_obs_set_def program.
-Simply make sure the appropriate template file 
-(kmf.template.ifc) is referenced 
-by mkmf_create_obs_set_def:
-
-
- 
-../../../mkmf/mkmf -p create_obs_set_def -t ../../../mkmf/mkmf.template.ifc -c"-Duse_netCDF" \

- -a "../../.." path_names_create_obs_set_def
-


-
-and then issue the following unix commands (from the work subdirectory):


-
-
-csh mkmf_create_obs_set_def

-make
-
-
-
-The first command generates an appropriate Makefile and
-the second results in the compilation of a series of Fortran90 modules which
-ultimately produces an executable file: 
-create_obs_set_def.
-Should you need to make any changes to the 
-DART/mkmf/mkmf.template.ifc, 
-you will need to regenerate the Makefile.  
-A series of .o and .mod files for each module compiled will also be 
-left in the work directory.
-You can proceed to create the other three programs needed to work with 
-L63 in DART as follows:
-
-
-
-csh mkmf_create_obs_sequence

-make

-csh mkmf_perfect_model_obs

-make

-csh mkmf_filter

-make
-


-
-The result (hopefully) is that four executables now 
-reside in your work directory.
-
-
-
-
-    
-
-    
-
-    
-
-    
-program purpose
create_obs_set_def specify a (set) of observation characteristics taken 
-        by a particular (set of) instruments
-    
create_obs_sequence specify the temporal attributes of the observation sets
-    
perfect_model_obs spinup, generate "true state" for synthetic observation experiments, ...
-    
filter perform experiments
-    
-
-
-
-
-
-
-Running Lorenz_63.
-
-This initial sequence of exercises includes detailed instructions 
-on how to work with the DART code and allows investigation of the 
-basic features of one of the most famous dynamical systems, the 
-3-variable Lorenz-63 model.
-The remarkable complexity of this simple model will also be used as 
-a case study to introduce a number of features of a simple ensemble 
-filter data assimilation system. 
-To perform a synthetic observation assimilation experiment 
-for the L63 model, the following steps must be performed 
-(an overview of the process is given first, 
-followed by detailed procedures for each step): 
-
-Experiment Overview
-
-   Integrate the L63 model for a long time

-   starting from arbitrary initial conditions to generate a model state 
-   that lies on the attractor. The ergodic nature of the L63 system 
-   means a 'lengthy' integration always converges to some point on 
-   the computer's finite precision representation of the model's 
-   attractor.


-
-   Generate a set of ensemble initial conditions

-   from which to start an assimilation. Since L63 is ergodic, the 
-   ensemble members can be designed to look like random samples from 
-   the model's 'climatological distribution'.  To generate an ensemble 
-   member, very small perturbations can be introduced to the state on 
-   the attractor generated by step 1. This perturbed state can then be 
-   integrated for a very long time until all memory of its initial 
-   condition can be viewed as forgotten. Any number of ensemble 
-   initial conditions can be generated by repeating this procedure.


-
-   Simulate a particular observing system

-   by creating an 'observation set definition', which requires 
-   interactive input describing the details of the observations,
-   but not the observations themselves.


-
-   Generate an 'observation sequence'

-   by integrating the model and using the information in the 
-   'observation set definition' file to create simulated observations.
-   This entails operating on the model state at the 
-   time of the observation with an appropriate forward operator 
-   (a function that operates on the model state vector to produce 
-   the expected value of the particular observation) and then adding 
-   a random sample from the observation error distribution specified 
-   in the observation set definition.  At the same time, diagnostic 
-   output about the 'true' state trajectory can be created.


-
-   Assimilate the synthetic observations

-   by running the filter; diagnostic output is generated.


-
-
-
-1. Integrate the L63 model for a 'long' time.
-perfect_model_obs integrates the model
-for all the times specified in the 'observation sequence definition' file.
-To this end, begin by creating an 'observation sequence definition' 
-file that spans a long time. Creating an 'observation sequence definition' 
-file is a two-step procedure involving 
-create_obs_set_def followed by 
-create_obs_sequence. After they are both run, it
-is necessary to integrate the model with perfect_model_obs.
-
-
-Create an observation set definition.
-create_obs_set_def creates an observation 
-set definition, the time-independent part of an observation sequence. 
-An observation set definition file only contains the 
-location, type, 
-and observational error characteristics 
-(normally just the diagonal observational error variance) 
-for a related set of observations. There are no actual observations,
-nor are there any times associated with the definition.
-For spin-up, we are only interested in integrating the L63 model, 
-not in generating any particular synthetic observations. 
-Begin by creating a minimal observation set definition.
-
-
-
-In general, for the low-order models, only a single observation set need
-be defined. Next, the number of individual scalar observations 
-(like a single surface pressure observation) in the set is needed. 
-To spin-up an initial condition for the L63 model, only a  
-single observation is needed. 
-Next, the error variance for this observation must be entered. 
-Since we are not interested in this observation having any impact 
-on an assimilation (it will only be used for spinning up the model 
-and the ensemble), enter a very large value for the error variance. 
-An observation with a very large error variance has essentially no 
-impact on deterministic filter assimilations like the default variety 
-implemented in DART.  Finally, the location and type of the 
-observation need to be defined.  For all types of models, 
-the most elementary form of synthetic observations are called 
-'identity' observations. These observations are generated simply 
-by adding a random sample from a specified observational error 
-distribution directly to the value of one of the state variables. 
-This defines the observation as being an identity observation of the 
-first state variable in the L63 model.
-The program will respond by terminating after generating a file 
-(generally named set_def.out) 
-that defines the single identity observation of the first 
-state variable of the L63 model. The following is a screenshot, 
-the user input looks like this.
-
-
-
--[unixprompt]$ ./create_obs_set_def
- create_obs_set_def attributes:
-    $source$
-    $revision: 2801 $
-    $date: 2007-04-04 22:11:48 -0600 (Wed, 04 Apr 2007) $
-     
- Input the filename for output of observation set_def_list? [set_def.out]
-set_def.out
- assim_model attributes:
-    $source$
-    $revision: 2801 $
-    $date: 2007-04-04 22:11:48 -0600 (Wed, 04 Apr 2007) $
- namelist read; values are
- sigma is     10.00000000000000
- r is     28.00000000000000
- b is     2.666666666666667
- deltat is    1.0000000000000000E-002
- output_state_vector is   T
- model attributes:
-    $source$
-    $revision: 2801 $
-    $date: 2007-04-04 22:11:48 -0600 (Wed, 04 Apr 2007) $
- model size is             3
- Input the number of unique observation sets you might define
-1
- How many observations in set             1
-1
- Defining observation             1
- Input error variance for this observation definition
-1000000
- Input an integer index if this is identity observation, else -1
-1
- set_def.out successfully created.
- Terminating normally.
-
-
-
-
-Create an observation sequence definition.
-create_obs_sequence creates an 'observation 
-sequence definition' by extending the 'observation set definition'
-with the temporal attributes of the observations.
-
-
-
-The first input is the name of the file created in the previous step, 
-i.e. the name of the observation set definition that you've 
-just created. 
-It is possible to create sequences in which the observation sets 
-are observed at regular intervals or irregularly in time. 
-Here, all we need is a sequence that takes observations over a 
-long period of time - indicated by entering a 1.
-Although the L63 system normally is defined as having a non-dimensional 
-time step, the DART system arbitrarily defines the model 
-timestep as being 3600 seconds. By declaring we have 1000 observations
-taken once per day, we create an observation sequence definition 
-spanning 24000 'model' timesteps; sufficient to spin-up the model 
-onto the attractor. Finally, enter a name for the 
-'observation sequence definition' file. Note again: there are no observation
-values present in this file. Just an observation type, location, time and the
-error characteristics. We are going to populate the observation sequence
-with the perfect_model_obs program.
-
-
-
--[thoar at ghotiol work]$ ./create_obs_sequence
- create_obs_sequence attributes:
-     
-    $source$
-    $revision: 2801 $
-    $date: 2007-04-04 22:11:48 -0600 (Wed, 04 Apr 2007) $
-     
- What is name of set_def_list? [set_def.out]
-set_def.out
- Setting times for obs_def             1
- To input a regularly repeating time sequence enter 1
- To enter an irregular list of times enter 2
-1
- Input number of observations in sequence
-1000
- Input time of initial ob in sequence in days and seconds
-1, 0
- Input period of obs in days and seconds
-1, 0
- time             1  is             0            1
- time             2  is             0            2
- time             3  is             0            3
-...
- time           998  is             0          998
- time           999  is             0          999
- time          1000  is             0         1000
- Input file name for output of obs_sequence? [obs_seq.in]
-obs_seq.in
-
-
-
-
-Initialize the model onto the attractor.
-perfect_model_obs can now advance the
-arbitrary initial state for 24,000 timesteps to move it onto the
-attractor.
-
-perfect_model_obs uses the Fortran90 namelist 
-input mechanism instead of (admittedly gory, but temporary) 
-interactive input.  In input.nml, the namelist for 
-perfect_model_obs the following values should be set:
-
-
-&perfect_model_obs_nml 

-   async = .false., 

-   obs_seq_in_file_name = "obs_seq.in", 

-   obs_seq_out_file_name = "obs_seq.out", 

-   start_from_restart = .false., 

-   output_restart = .true., 

-   restart_in_file_name = "perfect_ics", 

-   restart_out_file_name = "perfect_restart", 

-   init_time_days = 0, 

-   init_time_seconds = 0, 

-   output_interval = 1   /

-
-
-
-
-
-    
-
-
-    
-
-
-    
-
-
-    
-
-
-    
-
-
-    
-
-
-    
-
-
-    
-
-
-    
-
-namelist variable description
async Simply ignore this. Leave it set to '.false.'
obs_seq_in_file_name specifies the file name that results from running 
-        create_obs_sequence, i.e. the
-        'observation sequence definition' file.
obs_seq_out_file_name specifies the output file name containing the  
-        'observation sequence', finally populated with 
-        (perfect?) 'observations'.
start_from_restart When set to 'false', 
-        perfect_model_obs generates an 
-        arbitrary initial condition (which cannot be guaranteed 
-        to be on the L63 attractor).
output_restart When set to 'true', 
-        perfect_model_obs will record 
-        the model state at the end of this integration in the file 
-        named by restart_out_file_name.
restart_in_file_name is ignored when 'start_from_restart' is 'false'.
restart_out_file_name if output_restart is 'true', 
-        this specifies the name of the file containing the model 
-        state at the end of the integration.
init_time_xxxx the start time of the integration.
output_interval interval at which to save the model state.
-
-
-Executing perfect_model_obs will integrate the 
-model 24,000 steps and output the resulting state in the file 
-perfect_restart.
-
-perfect_model_obs
-
-
-
-
-2. Generate a set of ensemble initial conditions.
-The set of initial conditions for a 'perfect model' experiment is 
-created by taking the spun-up state of the model 
-(available in perfect_restart),
-running perfect_model_obs to generate
-the 'true state' of the experiment and a corresponding set of 
-observations, and then feeding the same initial spun-up state 
-and resulting observations into filter. 
-
-
-Generating ensemble initial conditions 
-is achieved by changing a perfect_model_obs namelist parameter, 
-copying perfect_restart to 
-perfect_ics, and 
-rerunning perfect_model_obs.
-This execution of perfect_model_obs 
-will advance the model state from 
-the end of the first 24,000 steps to the end of an additional 24,000 
-steps and place the final state in perfect_restart.
-
-
-
-&perfect_model_obs_nml 

-   async = .false., 

-   obs_seq_in_file_name = "obs_seq.in", 

-   obs_seq_out_file_name = "obs_seq.out", 

-   start_from_restart = .true., 

-   output_restart = .true., 

-   restart_in_file_name = "perfect_ics", 

-   restart_out_file_name = "perfect_restart", 

-   init_time_days = 0, 

-   init_time_seconds = 0, 

-   output_interval = 1  /
-
-

-
-cp perfect_restart perfect_ics

-perfect_model_obs
-
-A True_State.nc 
-file is also created. It contains the 'true' state of the integration.
-
-
-Generating the ensemble: is done with the program 
-filter, which also uses the Fortran90 namelist 
-mechanism for input.
-

-&filter_nml 

-   async = .false., 

-   ens_size = 20, 

-   cutoff = 0.0, 

-   cov_inflate = 1.0, 

-   start_from_restart = .false., 

-   output_restart = .true.,  

-   obs_sequence_file_name = "obs_seq.out", 

-   restart_in_file_name = "perfect_ics", 

-   restart_out_file_name = "filter_restart", 

-   init_time_days = 0, 

-   init_time_seconds = 0, 

-   output_state_ens_mean = .true.,  

-   output_state_ens_spread = .true.,  

-   num_output_ens_members = 20, 

-   output_interval = 1  /
-
-
-Only the non-obvious(?) entries will be discussed.
-
-
-
-
-    
-
-
-    
-
-
-    
-namelist variable description
ens_size Number of ensemble members. 
-    20 is sufficient for most of the exercises.
cutoff to limit the impact of an observation, set to 0.0
-        (i.e. spin-up)
cov_inflate A value of 1.0 results in no inflation.(spin-up)
-
-
-The filter is told to generate its own ensemble initial conditions 
-since start_from_restart is '.false.'. 
-However, it is important to note that the filter still makes use of 
-perfect_ics which is set to be the 
-restart_in_file_name. 
-This is the model state generated from the first 24,000 step model 
-integration by perfect_model_obs.
-Filter generates its ensemble initial conditions 
-by randomly perturbing the state variables of this state.
- 
-
-
-The arguments output_state_ens_mean
-and output_state_ens_spread are '.true.' so that 
-these quantities are output at every time for which there are 
-observations (once a day here) and 
-num_output_ens_members means that the same 
-diagnostic files, 
-Posterior_Diag.nc and Prior_Diag.nc 
-also contain values for all 20 ensemble members once a day. 
-Once the namelist is set, execute filter to 
-integrate the ensemble forward for 24,000 steps with the final ensemble 
-state written to the filter_restart.
-Copy the perfect_model_obs restart file
-perfect_restart (the `true state') to 
-perfect_ics, and the
-filter restart file 
-filter_restart to 
-filter_ics so that future assimilation experiments 
-can be initialized from these spun-up states.
-
-
-
-filter

-cp perfect_restart perfect_ics

-cp filter_restart filter_ics
-
-
-
-The spin-up of the ensemble can be viewed by examining the 
-output in the netCDF files True_State.nc 
-generated by perfect_model_obs and 
-Posterior_Diag.nc and Prior_Diag.nc 
-generated by filter. 
-To do this, see the detailed discussion of matlab diagnostics in Appendix I.
-
-
-
-
3. Simulate a particular observing system.
-
-Begin by using create_obs_set_def to 
-generate an observation set in which each of the 3 state variables 
-of L63 is observed with an observational error variance of 1.0 
-for each observation.  To do this, use the following input 
-sequence (the text including and after # is a comment and does 
-not need to be entered):
-
-
-
-    

@@ Diff output truncated at 40000 characters. @@

From nancy at ucar.edu  Thu Dec 12 15:11:25 2013
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Thu, 12 Dec 2013 15:11:25 -0700
Subject: [Dart-dev] [6674] DART/trunk/mkmf: updates to the mkmf files that
 somehow didn' t get committed
Message-ID: 

Revision: 6674
Author:   nancy
Date:     2013-12-12 15:11:24 -0700 (Thu, 12 Dec 2013)
Log Message:
-----------
updates to the mkmf files that somehow didn't get committed
before now.  mostly it was cleanups of the comment sections at
the top of each file, bringing it up to date with the current
versions of the compilers.  also made the default optimization
flag consistently just -O and not -O2; take the compiler default
for optimization without specifying a level.  made the default
flags in the debugging examples always use -g -- several did not
have it and instead had -O0.  removed the comment in the gfortran
mkmf file about fixsystem because it is called invisibly now
when needed.  

Modified Paths:
--------------
    DART/trunk/mkmf/mkmf.template
    DART/trunk/mkmf/mkmf.template.absoft.osx
    DART/trunk/mkmf/mkmf.template.g95
    DART/trunk/mkmf/mkmf.template.gfortran
    DART/trunk/mkmf/mkmf.template.intel.linux
    DART/trunk/mkmf/mkmf.template.intel.osx
    DART/trunk/mkmf/mkmf.template.lahey.linux
    DART/trunk/mkmf/mkmf.template.pathscale.linux
    DART/trunk/mkmf/mkmf.template.pgi.cray
    DART/trunk/mkmf/mkmf.template.pgi.linux
    DART/trunk/mkmf/mkmf.template.pgi.osx
    DART/trunk/mkmf/mkmf.template.sgi.altix
    DART/trunk/mkmf/mkmf.template.xlf.aix

-------------- next part --------------
Modified: DART/trunk/mkmf/mkmf.template
===================================================================
--- DART/trunk/mkmf/mkmf.template	2013-12-11 23:11:41 UTC (rev 6673)
+++ DART/trunk/mkmf/mkmf.template	2013-12-12 22:11:24 UTC (rev 6674)
@@ -9,74 +9,48 @@
 # typical use with mkmf
 # mkmf -t mkmf.template.xxxx ...
 #
-# Most likely NETCDF (and maybe LIBS) will need to be customized for your site
 #
+# Suggested debugging flags:
+#  -g                  add debugging information to executable
+#  -fbacktrace         runtime errors try to print out a stack backtrace
+#  -fbounds-check      add runtime-checking for out-of-range array indices
+#  -ffpe-trap=invalid,zero,overflow
+#                      stop on floating point errors
 #
-# Building DART with open-source software:
+#  earlier versions of this mkmf file listed 'precision' as one of the options on
+#  the fpe-trap line.  this is not recommended anymore as some of the gfortran internal
+#  routines will trap, as well as some perfectly valid DART computations.
 #
-# All the parts (except matlab, which is optional and only used to display results)
-# needed to build and run the DART package are now possible to get free from
-# the open-source community.  To compile and run DART, you will need:
+# Generally not needed but possibly useful for non-DART code:
 #
+# -ffree-form          forces input file to be read as free format regardless
+#                      of what file extension it has.
 #
-# 1. The GNU GCC 4.2.0 version of the gfortran compiler.  See this web page for
-#    information on supported platforms and downloads:
-#      http://gcc.gnu.org/wiki/GFortran
+# -fdefault-real-8     force all real variables to be real*8.  not needed for DART code
+#                      since all real variables in DART are declared with a size.
 #
-#    (Note that there is a separate G95 project which distributes an alternate
-#    open-source fortran distribution, and I have heard that others have
-#    successfully compiled other fortran code with that compiler, but we have
-#    not tried it with DART yet.)
+#    NOTE: Some previous versions of the gfortran compiler (including 4.1.2)
+#    changed the record marker size to 8 bytes, which made binary files written
+#    with the 'unformatted' option unreadable by programs compiled with other
+#    compilers.  Later versions of the compiler changed the default back to 4 bytes.
+#    If you have a version that defaults to 8 byte record markers, use this 
+#    compile time flag:
+#       -frecord-marker=4
+#    If you have files written by older versions of the gfortran compiler that
+#    cannot be read now, try this compile time flag:
+#       -frecord-marker=8 
 #
-#    NOTE: The 4.1.2 compiler made the HORRIBLE choice of changing the default
-#    record header size for unformatted writes such that it was incompatible
-#    with every existing binary file. Specifying -frecord-marker=4 is crucial
-#    to have any hope of success.
+# Convert big-endian or little-endian binary files at runtime:
 #
-# 2. The netCDF software library package.  See:
-#      http://www.unidata.ucar.edu/software/netcdf
+# setenv GFORTRAN_CONVERT_UNIT 'big_endian'
+#    Treats ALL units as big_endian
 #
-#    The 3.6.2 version compiled for us with this:
+# setenv GFORTRAN_CONVERT_UNIT 'big_endian;native:10-20'
+#    Treats units 10-20 as big_endian but the rest are 'native' 
 #
-#     ./configure CC=gcc FC=gfortran
-#     make check
-#     make install
-#
-#    You can add the argument --prefix=/dir to configure to make the install
-#    location for the includes and libs someplace other than /usr/local.
-#
-#
-# If you want to try the *optional* parallel execution option, you will
-# need a version of the MPI libs.  There are at least two open source options:
-#
-# 3. For parallel execution, OpenMPI 1.2 from:
-#       http://www.open-mpi.org/
-#
-#     or mpich from:
-#       http://http://www-unix.mcs.anl.gov/mpi/mpich/
-#
-# Note that MPI IS NOT REQUIRED to build and run DART.
-#
-#
-# Possibly useful flags:
-#
-# -ffree-form          forces input file to be read as free format regardless
-#                      of what file extension is has.
-#
-# -fdefault-real-8     force all real variables to be real*8.
-#
-# -ffpe-trap=invalid,overflow,precision,denormal,underflow
-#
-#
-# NOTE: there is no compile-time convert endian flag. It is a run-time option.
+# for more information on unit conversions:
 # http://gcc.gnu.org/onlinedocs/gfortran/GFORTRAN_005fCONVERT_005fUNIT.html#GFORTRAN_005fCONVERT_005fUNIT
-#       To treat units 10-20 as big_endian but the rest are 'native' ...
-#       setenv GFORTRAN_CONVERT_UNIT 'big_endian;native:10-20'
 #
-#       To treat ALL units as big_endian (the 10-20 is meaningless in this instance):
-#       setenv GFORTRAN_CONVERT_UNIT 'big_endian;big_endian:10-20'
-#
-# IF YOU HAVE MORE CURRENT COMPILER INFORMATION, PLEASE SHARE IT WITH US.
 
 MPIFC = mpif90
 MPILD = mpif90
@@ -109,7 +83,7 @@
 FFLAGS  = -O2 -ffree-line-length-none $(INCS)
 LDFLAGS = $(FFLAGS) $(LIBS)
 
-#FFLAGS = -O0 -fbounds-check -frecord-marker=4 -ffpe-trap=invalid -ffree-line-length-none $(INCS)
+#FFLAGS = -g -ffree-line-length-none -fbounds-check -fbacktrace -ffpe-trap=invalid,zero,overflow $(INCS)
 
 # 
 # $URL$

Modified: DART/trunk/mkmf/mkmf.template.absoft.osx
===================================================================
--- DART/trunk/mkmf/mkmf.template.absoft.osx	2013-12-11 23:11:41 UTC (rev 6673)
+++ DART/trunk/mkmf/mkmf.template.absoft.osx	2013-12-12 22:11:24 UTC (rev 6674)
@@ -94,13 +94,13 @@
 
 INCS =   $(NETCDF)/include
 LIBS = -L$(NETCDF)/lib -lnetcdff -lnetcdf
-FFLAGS  = -YEXT_NAMES=LCS -YEXT_SFX=_ -en -altiVec -O0 -Rb -Rc -g -p$(INCS)
+FFLAGS  = -YEXT_NAMES=LCS -YEXT_SFX=_ -altiVec -O -p$(INCS)
 LDFLAGS = -unixlib $(FFLAGS) $(LIBS)
 
 # alternate (sometimes useful) fortran flags invocations
-#FFLAGS = -YEXT_NAMES=LCS -YEXT_SFX=_ -en -altiVec -O0 -Rb -Rc -p$(INCS)
-#FFLAGS = -YEXT_NAMES=LCS -YEXT_SFX=_ -en -altiVec -O0 -N113 -f free -Rb -Rc -p$(INCS) -I$(INCS)
-#FFLAGS = -YEXT_NAMES=LCS -YEXT_SFX=_ -en -altiVec -O0 -Rb -Rc -N26 -p$(INCS) -I$(INCS)
+#FFLAGS = -YEXT_NAMES=LCS -YEXT_SFX=_ -en -g -Rb -Rc -p$(INCS)
+#FFLAGS = -YEXT_NAMES=LCS -YEXT_SFX=_ -en -altiVec -O -N113 -f free -Rb -Rc -p$(INCS) -I$(INCS)
+#FFLAGS = -YEXT_NAMES=LCS -YEXT_SFX=_ -en -altiVec -O -Rb -Rc -N26 -p$(INCS) -I$(INCS)
 
 # 
 # $URL$

Modified: DART/trunk/mkmf/mkmf.template.g95
===================================================================
--- DART/trunk/mkmf/mkmf.template.g95	2013-12-11 23:11:41 UTC (rev 6673)
+++ DART/trunk/mkmf/mkmf.template.g95	2013-12-12 22:11:24 UTC (rev 6674)
@@ -1,4 +1,4 @@
-# Template for GNU g95 on Linux or Mac OSX
+# Template for the g95 compiler on Linux or Mac OSX
 #
 # DART software - Copyright 2004 - 2013 UCAR. This open source software is
 # provided by UCAR, "as is", without charge, subject to all terms of use at
@@ -9,49 +9,10 @@
 # typical use with mkmf
 # mkmf -t mkmf.template.xxxx ...
 #
-# Most likely NETCDF (and maybe LIBS) will need to be customized for your site
+# This template is for the g95 version of fortran.  This is NOT the GNU
+# gfortran compiler; this is a compiler from a separate project.
+# see http://g95.sourceforge.net for more info.
 #
-#
-# Building DART with open-source software:
-#
-# All the parts (except matlab, which is optional and only used to display results)
-# needed to build and run the DART package are now possible to get free from
-# the open-source community.  To compile and run DART, you will need:
-#
-#
-# 1. The g95 compiler.  See this web page for
-#    information on supported platforms and downloads:
-#      http://g95.sourceforge.net/
-#
-#    (Note that the g95 compiler is a separate project from the 'gfortran'
-#    compiler.  gfortran is part of the GNU compiler development efforts;
-#    g95 is a separately developed and supported project.)
-#
-#
-# 2. The netCDF software library package.  See:
-#      http://www.unidata.ucar.edu/software/netcdf
-#
-#    The 3.6.2 version compiled for us with this:
-#
-#     ./configure CC=gcc FC=g95
-#     make check
-#     make install
-#
-#    You can add the argument --prefix=/dir to configure to make the install
-#    location for the includes and libs someplace other than /usr/local.
-#
-#
-# If you want to try the *optional* parallel execution option, you will
-# need a version of the MPI libs.  There are at least two open source options:
-#
-# 3. For parallel execution, OpenMPI 1.2 from:
-#       http://www.open-mpi.org/
-#
-#     or mpich from:
-#       http://http://www-unix.mcs.anl.gov/mpi/mpich/
-#
-# Note that MPI IS NOT REQUIRED to build and run DART.
-#
 # IF YOU HAVE MORE CURRENT COMPILER INFORMATION, PLEASE SHARE IT WITH US.
 
 MPIFC = mpif90

Modified: DART/trunk/mkmf/mkmf.template.gfortran
===================================================================
--- DART/trunk/mkmf/mkmf.template.gfortran	2013-12-11 23:11:41 UTC (rev 6673)
+++ DART/trunk/mkmf/mkmf.template.gfortran	2013-12-12 22:11:24 UTC (rev 6674)
@@ -9,74 +9,48 @@
 # typical use with mkmf
 # mkmf -t mkmf.template.xxxx ...
 #
-# Most likely NETCDF (and maybe LIBS) will need to be customized for your site
 #
+# Suggested debugging flags:
+#  -g                  add debugging information to executable
+#  -fbacktrace         runtime errors try to print out a stack backtrace
+#  -fbounds-check      add runtime-checking for out-of-range array indices
+#  -ffpe-trap=invalid,zero,overflow
+#                      stop on floating point errors
 #
-# Building DART with open-source software:
+#  earlier versions of this mkmf file listed 'precision' as one of the options on
+#  the fpe-trap line.  this is not recommended anymore as some of the gfortran internal
+#  routines will trap, as well as some perfectly valid DART computations.
 #
-# All the parts (except matlab, which is optional and only used to display results)
-# needed to build and run the DART package are now possible to get free from
-# the open-source community.  To compile and run DART, you will need:
+# Generally not needed but possibly useful for non-DART code:
 #
+# -ffree-form          forces input file to be read as free format regardless
+#                      of what file extension it has.
 #
-# 1. The GNU GCC 4.2.0 version of the gfortran compiler.  See this web page for
-#    information on supported platforms and downloads:
-#      http://gcc.gnu.org/wiki/GFortran
+# -fdefault-real-8     force all real variables to be real*8.  not needed for DART code
+#                      since all real variables in DART are declared with a size.
 #
-#    (Note that there is a separate G95 project which distributes an alternate
-#    open-source fortran distribution, and I have heard that others have
-#    successfully compiled other fortran code with that compiler, but we have
-#    not tried it with DART yet.)
+#    NOTE: Some previous versions of the gfortran compiler (including 4.1.2)
+#    changed the record marker size to 8 bytes, which made binary files written
+#    with the 'unformatted' option unreadable by programs compiled with other
+#    compilers.  Later versions of the compiler changed the default back to 4 bytes.
+#    If you have a version that defaults to 8 byte record markers, use this 
+#    compile time flag:
+#       -frecord-marker=4
+#    If you have files written by older versions of the gfortran compiler that
+#    cannot be read now, try this compile time flag:
+#       -frecord-marker=8 
 #
-#    NOTE: The 4.1.2 compiler made the HORRIBLE choice of changing the default
-#    record header size for unformatted writes such that it was incompatible
-#    with every existing binary file. Specifying -frecord-marker=4 is crucial
-#    to have any hope of success.
+# Convert big-endian or little-endian binary files at runtime:
 #
-# 2. The netCDF software library package.  See:
-#      http://www.unidata.ucar.edu/software/netcdf
+# setenv GFORTRAN_CONVERT_UNIT 'big_endian'
+#    Treats ALL units as big_endian
 #
-#    The 3.6.2 version compiled for us with this:
+# setenv GFORTRAN_CONVERT_UNIT 'big_endian;native:10-20'
+#    Treats units 10-20 as big_endian but the rest are 'native' 
 #
-#     ./configure CC=gcc FC=gfortran
-#     make check
-#     make install
-#
-#    You can add the argument --prefix=/dir to configure to make the install
-#    location for the includes and libs someplace other than /usr/local.
-#
-#
-# If you want to try the *optional* parallel execution option, you will
-# need a version of the MPI libs.  There are at least two open source options:
-#
-# 3. For parallel execution, OpenMPI 1.2 from:
-#       http://www.open-mpi.org/
-#
-#     or mpich from:
-#       http://http://www-unix.mcs.anl.gov/mpi/mpich/
-#
-# Note that MPI IS NOT REQUIRED to build and run DART.
-#
-#
-# Possibly useful flags:
-#
-# -ffree-form          forces input file to be read as free format regardless
-#                      of what file extension is has.
-#
-# -fdefault-real-8     force all real variables to be real*8.
-#
-# -ffpe-trap=invalid,overflow,precision,denormal,underflow
-#
-#
-# NOTE: there is no compile-time convert endian flag. It is a run-time option.
+# for more information on unit conversions:
 # http://gcc.gnu.org/onlinedocs/gfortran/GFORTRAN_005fCONVERT_005fUNIT.html#GFORTRAN_005fCONVERT_005fUNIT
-#       To treat units 10-20 as big_endian but the rest are 'native' ...
-#       setenv GFORTRAN_CONVERT_UNIT 'big_endian;native:10-20'
 #
-#       To treat ALL units as big_endian (the 10-20 is meaningless in this instance):
-#       setenv GFORTRAN_CONVERT_UNIT 'big_endian;big_endian:10-20'
-#
-# IF YOU HAVE MORE CURRENT COMPILER INFORMATION, PLEASE SHARE IT WITH US.
 
 MPIFC = mpif90
 MPILD = mpif90
@@ -109,7 +83,7 @@
 FFLAGS  = -O2 -ffree-line-length-none $(INCS)
 LDFLAGS = $(FFLAGS) $(LIBS)
 
-#FFLAGS = -O0 -fbounds-check -frecord-marker=4 -ffpe-trap=invalid -ffree-line-length-none $(INCS)
+#FFLAGS = -g -ffree-line-length-none -fbounds-check -fbacktrace -ffpe-trap=invalid,zero,overflow $(INCS)
 
 # 
 # $URL$

Modified: DART/trunk/mkmf/mkmf.template.intel.linux
===================================================================
--- DART/trunk/mkmf/mkmf.template.intel.linux	2013-12-11 23:11:41 UTC (rev 6673)
+++ DART/trunk/mkmf/mkmf.template.intel.linux	2013-12-12 22:11:24 UTC (rev 6674)
@@ -88,7 +88,12 @@
 #     -assume  byterecl ... more 'industry-standard' direct-access behavior
 #              controls what units the RECL (record length) specifier returns.
 #
+# Runtime environment variables that influence the compiler behavior:
 #
+# Make output lines for fortran write statements longer without wrapping:
+#   setenv FORT_FMT_RECL 512  (or any length)
+#
+#
 # IF YOU HAVE MORE CURRENT COMPILER INFORMATION, PLEASE SHARE IT WITH US.
 
 MPIFC = mpif90

Modified: DART/trunk/mkmf/mkmf.template.intel.osx
===================================================================
--- DART/trunk/mkmf/mkmf.template.intel.osx	2013-12-11 23:11:41 UTC (rev 6673)
+++ DART/trunk/mkmf/mkmf.template.intel.osx	2013-12-12 22:11:24 UTC (rev 6674)
@@ -9,22 +9,91 @@
 # typical use with mkmf
 # mkmf -t mkmf.template.xxxx ...
 #
-# NOTE: The intel compiler can provide a lot more
-#       information if you LEAVE the object and module files intact.
-#       Do not remove the *.o and *.mod files when debugging code.
+# FFLAGS   useful for DEBUGGING. NOTE: The intel compiler can provide a lot more
+#          information if you LEAVE the object and module files intact.
+#          Do not remove the *.o and *.mod files when debugging code.
 #
-# Building DART with the commercial Intel compiler for the iMacs:
+#     -g       include debugging information.  these are all synonyms.
+#     -debug full
+#     -debug all
+#     -O0      setting -g will make this the default (no optimization).
+#              it is possible to set -g and then explicitly set -O2 if
+#              the behavior being debugged depends on optimization changes.
+#     -ftrapuv   traps if a local variable is used before being set
+#     -C       enables all runtime checks.  -C and -check all are synonyms.
+#     -check all
+#     -check     enables/disables more specific runtime checks.
+#           keywords:  [arg_temp_created,bounds,overflow,format,pointers,uninit]
+#     -warn   the level of warning messages issued.
+#           keywords:  [alignments, argument_checking, declarations,
+#                      errors, fileopt, general, ignore_loc,
+#                      stderrors, truncated_source, uncalled,
+#                      uninitialized, unused, usage, all]
+#     -fp-stack-check  catches conditions where the FP stack is not correct.
+#           Typically this is when a real function is called as if it were a
+#           subroutine, OR a subroutine is called as if it were a function (return
+#           values left of FP stack OR too much data is taken off the FP stack)
+#     -vec-reportN  controls how much diagnostic output is printed about
+#                   loops vectorized by the compiler. N = 0 is silent,
+#                   N can have values up to 5.
+#     -traceback    tells the compiler to generate extra information in the
+#                   object file to provide source file traceback information
+#                   when a severe error occurs at run time
 #
-# You will need to have a version of the (free) netCDF software
-# library package:
+# FFLAGS   useful for bitwise reproducibility and accuracy control
+#          (these will slow down performance to various degrees)
+#     -fp-model precise    control how floating point roundoff is done so it is
+#                          reproducible from run to run.  in simple tests this
+#                          flag alone was enough to create bitwise reproducible
+#                          code but slowed execution significantly.
+#     -ftz        'flush to zero' underflows result in zero.  set by default if
+#                 any -O other than -O0 set, or if -fpe0 or -fpe1 set.
+#     -fpeN       controls floating point exception handling.  -fpe0 rounds underflow
+#                 to zero and traps on any other exception type.
+#     -pc80       set internal FPU precision to 64 bit significand
+#                 (default is -pc64 with 53 internal bits)
 #
-#      http://www.unidata.ucar.edu/software/netcdf
+# FFLAGS   useful for production
+#     -O2        default.  optimize without too much unrepeatable numerical games
+#     -O3        more aggressive optimizations.  check numerical differences
+#                before using this indiscriminately.
+#     -O1        if you get compile-time errors about out of memory or unable to
+#                complete compilation because of complexity, try lowering the
+#                optimization level on the offending source files.
+#     -ipo       enable optimizations between routines in separate source files
+#     -heap-arrays 10    allocate large arrays from the heap instead of putting them
+#                on the stack.  the number is the limit in KB for when arrays
+#                move from the stack to the heap.  this can help if you get stack
+#                overflow errors and cannot increase the stack size more.
+#                allocating from the stack is faster, but it's usually a smaller
+#                size than the heap.
+#     -x, -m, -ax, -mcode, -march   all these flags tell the compiler to generate
+#                processor-specific or vector instructions.  either 'man ifort' or
+#                ifort --help to see what the current list of options are and
+#                which have priority over the others.
+#                (for those running on yellowstone, -axavx will enable the advanced
+#                vector instructions available on the sandy bridge processors.)
 #
+# FFLAGS   possibly useful, not normally used by DART
+#     -fpp     run Fortran preprocessor on source files prior to compilation
+#     -free    interpret source as free-format, regardless of file extension
+#     -r8      specify default real size.  note that for DART we use explicit
+#              types on all our real values so this will not change anything
+#              inside DART.   see DART/common/types_mod.f90 if you must run
+#              with single precision reals.
+#     -convert big_endian         useful if you're on the wrong architecture.
+#              however this controls both reading and writing so you can't
+#              use it as a conversion mechanism unless you write files out
+#              in ascii format.  applies to all unformatted fortran i/o.
+#     -assume  byterecl ... more 'industry-standard' direct-access behavior
+#              controls what units the RECL (record length) specifier returns.
 #
-# users have had problems with the default stack size on OS X.
-# the -Wl,-stack_size argument below increases the stack large
-# enough to run large models.
+# Runtime environment variables that influence the compiler behavior:
 #
+# Make output lines for fortran write statements longer without wrapping:
+#   setenv FORT_FMT_RECL 512  (or any length)
+#
+#
 # IF YOU HAVE MORE CURRENT COMPILER INFORMATION, PLEASE SHARE IT WITH US.
 
 MPIFC = mpif90
@@ -57,13 +126,22 @@
 LIBS = -L$(NETCDF)/lib -lnetcdff -lnetcdf
 
 # for Intel 9.x:
-FFLAGS  = $(INCS) -O2
-LDFLAGS = $(INCS) -Wl,-stack_size,10000000 $(LIBS)
+#FFLAGS  = $(INCS) -O2
+#LDFLAGS = $(INCS) -Wl,-stack_size,10000000 $(LIBS)
 
-# for Intel 10.x:
-#FFLAGS  = $(INCS) -O2 -m64 -heap-arrays -vec-report0 -fpe0
-#LDFLAGS = $(INCS) $(LIBS)
+# for Intel 10.x and beyond:
+FFLAGS  = $(INCS) -O2 -m64 -heap-arrays -vec-report0 
+LDFLAGS = $(INCS) $(LIBS)
 
+# for development or debugging, use this instead:
+# FFLAGS = -g -C -check noarg_temp_created -fpe0 -vec-report0 \
+#          -fp-model precise  -ftrapuv -traceback \
+#          -warn argument_checking,declarations,uncalled,unused $(INCS)
+#
+# If you get this error: libimf.so: warning: warning: feupdateenv is not implemented
+# try adding: -limf -lm to your LIBS line.
+
+
 # 
 # $URL$
 # $Revision$

Modified: DART/trunk/mkmf/mkmf.template.lahey.linux
===================================================================
--- DART/trunk/mkmf/mkmf.template.lahey.linux	2013-12-11 23:11:41 UTC (rev 6673)
+++ DART/trunk/mkmf/mkmf.template.lahey.linux	2013-12-12 22:11:24 UTC (rev 6674)
@@ -20,7 +20,7 @@
 #    -O2
 #    -ap                 ensure consistent arithmetic precision
 #    -Wa,--32            pass on to loader ... (32 bit compile)
-#    --trap  trap ndp exceptions
+#    --trap              trap ndp exceptions
 #    --verbose
 #    --warn
 #    --wide
@@ -82,7 +82,7 @@
 
 INCS = -I$(NETCDF)/include
 LIBS = -L$(NETCDF)/lib -lnetcdff -lnetcdf
-FFLAGS  = -Wa,--32 --trap --wide --o2 $(INCS)
+FFLAGS  = -Wa,--32 --wide --o2 $(INCS)
 LDFLAGS = $(FFLAGS) $(LIBS)
 
 # for debugging or development, here are some suggested flags:

Modified: DART/trunk/mkmf/mkmf.template.pathscale.linux
===================================================================
--- DART/trunk/mkmf/mkmf.template.pathscale.linux	2013-12-11 23:11:41 UTC (rev 6673)
+++ DART/trunk/mkmf/mkmf.template.pathscale.linux	2013-12-12 22:11:24 UTC (rev 6674)
@@ -1,5 +1,4 @@
-# Template for Pathscale 2.0 f90 Compiler on a Linux cluster
-#  (tested to the NCAR machine 'lightning' - an Opteron cluster)
+# Template for Pathscale f90 Compiler on a Linux cluster
 #
 # DART software - Copyright 2004 - 2013 UCAR. This open source software is
 # provided by UCAR, "as is", without charge, subject to all terms of use at
@@ -28,11 +27,6 @@
 # IF YOU HAVE MORE CURRENT COMPILER INFORMATION, PLEASE SHARE IT WITH US.
 
 #----------------------------------------------------------------------
-# if the pathScale module is loaded, these things are already properly set.
-#MPI_HOME=/contrib/mpich-gm/1.2.6..13b-pathscale-2.0-64
-#MPIFC=$(MPI_HOME)/bin/mpif90
-#MPILD=$(MPI_HOME)/bin/mpif90
-#----------------------------------------------------------------------
 
 MPIFC = mpif90
 MPILD = mpif90
@@ -62,11 +56,11 @@
 
 INCS = -I$(NETCDF)/include
 LIBS = -L$(NETCDF)/lib -lnetcdff -lnetcdf
-FFLAGS  = -O2 $(INCS)
+FFLAGS  = -O $(INCS)
 LDFLAGS = $(FFLAGS) $(LIBS)
 
 # for development/debugging, use these flags instead:
-#FFLAGS = -Wuninitialized -ffortran-bounds-check -fullwarn -O0 -I$(NETCDF)/include
+#FFLAGS = -Wuninitialized -ffortran-bounds-check -fullwarn -g -I$(NETCDF)/include
 
 # 
 # $URL$

Modified: DART/trunk/mkmf/mkmf.template.pgi.cray
===================================================================
--- DART/trunk/mkmf/mkmf.template.pgi.cray	2013-12-11 23:11:41 UTC (rev 6673)
+++ DART/trunk/mkmf/mkmf.template.pgi.cray	2013-12-12 22:11:24 UTC (rev 6674)
@@ -71,11 +71,11 @@
 
 INCS = -I$(NETCDF)/include
 LIBS = -L$(NETCDF)/lib -lnetcdff -lnetcdf
-FFLAGS  = -O2 $(INCS)
+FFLAGS  = -O $(INCS)
 LDFLAGS = $(INCS) $(LIBS)
 
 # for development or debugging, use this for flags:
-#FFLAGS = -O0 -Ktrap=fp -pc 64 $(INCS)
+#FFLAGS = -g -Ktrap=fp -pc 64 $(INCS)
 
 # 
 # $URL$

Modified: DART/trunk/mkmf/mkmf.template.pgi.linux
===================================================================
--- DART/trunk/mkmf/mkmf.template.pgi.linux	2013-12-11 23:11:41 UTC (rev 6673)
+++ DART/trunk/mkmf/mkmf.template.pgi.linux	2013-12-12 22:11:24 UTC (rev 6674)
@@ -73,11 +73,11 @@
 
 INCS = -I$(NETCDF)/include
 LIBS = -L$(NETCDF)/lib -lnetcdff -lnetcdf
-FFLAGS  = -O2 -Mextend $(INCS)
+FFLAGS  = -O $(INCS)
 LDFLAGS = $(FFLAGS) $(LIBS)
 
 # for development or debugging, use this for flags:
-#FFLAGS = -O0 -C -Ktrap=fp -pc 64 $(INCS)
+#FFLAGS = -g -C -Ktrap=fp -pc 64 $(INCS)
 
 # 
 # $URL$

Modified: DART/trunk/mkmf/mkmf.template.pgi.osx
===================================================================
--- DART/trunk/mkmf/mkmf.template.pgi.osx	2013-12-11 23:11:41 UTC (rev 6673)
+++ DART/trunk/mkmf/mkmf.template.pgi.osx	2013-12-12 22:11:24 UTC (rev 6674)
@@ -1,6 +1,4 @@
 # template for PGI f90 Compiler on Mac OS X
-# (at the time of the latest DART release there was a PGI beta compiler
-#   available for Intel-based Macs)
 #
 # DART software - Copyright 2004 - 2013 UCAR. This open source software is
 # provided by UCAR, "as is", without charge, subject to all terms of use at
@@ -70,11 +68,11 @@
 
 INCS = -I$(NETCDF)/include
 LIBS = -L$(NETCDF)/lib -lnetcdff -lnetcdf
-FFLAGS  = -O2 $(INCS)
+FFLAGS  = -O $(INCS) 
 LDFLAGS = $(FFLAGS) $(LIBS)
 
 # for development or debugging, use this for flags:
-#FFLAGS = -O0 -Ktrap=fp -pc 64 $(INCS)
+#FFLAGS = -g -Ktrap=fp -pc 64 $(INCS)
 
 # 
 # $URL$

Modified: DART/trunk/mkmf/mkmf.template.sgi.altix
===================================================================
--- DART/trunk/mkmf/mkmf.template.sgi.altix	2013-12-11 23:11:41 UTC (rev 6673)
+++ DART/trunk/mkmf/mkmf.template.sgi.altix	2013-12-12 22:11:24 UTC (rev 6674)
@@ -1,6 +1,4 @@
-# Template for SGI Altix systems
-# (Altix clusters are based on Intel chips,
-#  not MIPS chips like earlier SGI systems.)
+# Template for SGI Altix systems (which are Intel-processor based)
 #
 # DART software - Copyright 2004 - 2013 UCAR. This open source software is
 # provided by UCAR, "as is", without charge, subject to all terms of use at
@@ -104,6 +102,12 @@
 #     -assume  byterecl ... more 'industry-standard' direct-access behavior
 #              controls what units the RECL (record length) specifier returns.
 #
+# Runtime environment variables that influence the compiler behavior:
+#
+# Make output lines for fortran write statements longer without wrapping:
+#   setenv FORT_FMT_RECL 512  (or any length)
+#
+
 # IF YOU HAVE MORE CURRENT COMPILER INFORMATION, PLEASE SHARE IT WITH US.
 
 MPIFC = ifort

Modified: DART/trunk/mkmf/mkmf.template.xlf.aix
===================================================================
--- DART/trunk/mkmf/mkmf.template.xlf.aix	2013-12-11 23:11:41 UTC (rev 6673)
+++ DART/trunk/mkmf/mkmf.template.xlf.aix	2013-12-12 22:11:24 UTC (rev 6674)
@@ -70,10 +70,10 @@
 
 INCS = -I/usr/local/lib64/r4i4 -I/usr/local/include
 LIBS = -L/usr/local/lib64/r4i4 -lnetcdf
-FFLAGS  = -qsuffix=f=f90:cpp=F90 -q64 -b64 -qarch=auto -qmaxmem=-1 -O2 $(INCS)
+FFLAGS  = -qsuffix=f=f90:cpp=F90 -q64 -b64 -qarch=auto -qmaxmem=-1 -O $(INCS)
 LDFLAGS = $(FFLAGS) $(LIBS)
 
-#FFLAGS = -qsuffix=f=f90:cpp=F90 -q64 -b64 -qarch=auto -qmaxmem=-1 -O0 -C -g -qfullpath \
+#FFLAGS = -qsuffix=f=f90:cpp=F90 -q64 -b64 -qarch=auto -qmaxmem=-1 -C -g -qfullpath \
 #         -qsigtrap=xl__trcedump -qflttrap=ov:zero:inv:en $(INCS)
 
 # 

From nancy at ucar.edu  Fri Dec 13 11:00:46 2013
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Fri, 13 Dec 2013 11:00:46 -0700
Subject: [Dart-dev] [6676] DART/trunk/doc/html/Lanai_release.html: fix the
 dates of the releases and remove the SVN revision
Message-ID: 

Revision: 6676
Author:   nancy
Date:     2013-12-13 11:00:45 -0700 (Fri, 13 Dec 2013)
Log Message:
-----------
fix the dates of the releases and remove the SVN revision
numbers because they change as files are committed.

Modified Paths:
--------------
    DART/trunk/doc/html/Lanai_release.html

-------------- next part --------------
Modified: DART/trunk/doc/html/Lanai_release.html
===================================================================
--- DART/trunk/doc/html/Lanai_release.html	2013-12-13 00:22:59 UTC (rev 6675)
+++ DART/trunk/doc/html/Lanai_release.html	2013-12-13 18:00:45 UTC (rev 6676)
@@ -1958,9 +1958,9 @@
 Non-backwards Compatible Changes
 
 
-Changes in the Lanai release (SVN revision number NNNN, dd mmm 2013)
+Changes in the Lanai release (13 Dec 2013)
 which are not backwards compatible
-with the Kodiak release (SVN revision number 5018, 15 June 2011):
+with the Kodiak release (30 June 2011):
 
 
 

From nancy at ucar.edu  Fri Dec 13 11:51:46 2013
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Fri, 13 Dec 2013 11:51:46 -0700
Subject: [Dart-dev] [6678] DART/trunk/doc/html/Lanai_release.html: update
 compiler list and links.
Message-ID: 

Revision: 6678
Author:   nancy
Date:     2013-12-13 11:51:46 -0700 (Fri, 13 Dec 2013)
Log Message:
-----------
update compiler list and links.

Modified Paths:
--------------
    DART/trunk/doc/html/Lanai_release.html

-------------- next part --------------
Modified: DART/trunk/doc/html/Lanai_release.html
===================================================================
--- DART/trunk/doc/html/Lanai_release.html	2013-12-13 18:02:27 UTC (rev 6677)
+++ DART/trunk/doc/html/Lanai_release.html	2013-12-13 18:51:46 UTC (rev 6678)
@@ -156,7 +156,7 @@
 
 Matlab®: A set of 
 Matlab® scripts designed to 
-produce graphical diagnostics from DART netCDF output files are also part
+produce graphical diagnostics from DART. netCDF output files are also part
 of the DART project.


 
 MPI: The DART system includes an MPI
@@ -284,18 +284,16 @@
 Requirements: an F90 Compiler
 
 
-The DART software has been successfully built on several Linux/x86
-platforms with several versions of the 
-Intel Fortran
-Compiler for Linux, which (at one point) is/was free for individual 
-scientific use.  Also Intel Fortran for Mac OSX.
-It has also been built and successfully run with several 
-versions of each of the following:
+The DART software has been successfully built on many Linux,
+OS/X, and supercomputer platforms with compilers that include
+GNU Fortran Compiler ("gfortran")
+(free), 
+Intel Fortran
+Compiler for Linux and Mac OS/X,
 Portland Group Fortran Compiler, 
 Lahey Fortran Compiler, 
 Pathscale Fortran Compiler, 
-GNU Fortran 95 Compiler ("gfortran"), 
-Absoft Fortran 90/95 Compiler (Mac OSX). 
+and the Cray native compiler.
 Since recompiling the code is a necessity to experiment
 with different models, there are no binaries to distribute.
 
@@ -329,9 +327,6 @@
 the netCDF home page: 
 
 http://www.unidata.ucar.edu/packages/netcdf/ 
-Pay particular attention to the compiler-specific patches that must 
-be applied for the Intel Fortran Compiler. (Or the PG compiler, for
-that matter.)
 
 
 

From thoar at ucar.edu  Mon Dec 16 07:30:21 2013
From: thoar at ucar.edu (Tim Hoar)
Date: Mon, 16 Dec 2013 08:30:21 -0600
Subject: [Dart-dev] [Dart-users] The Lanai release of DART is here
In-Reply-To: <52AB6A55.9030304@ucar.edu>
References: <52AB6A55.9030304@ucar.edu>
Message-ID: 


Hurrah! Welcome news indeed.
That will take some of the sting at having to come back to work. 

Tim

P.S. Flight delayed out of Houston. Will not arrive in boulder till 2ish, so I'll just wait till tomorrow to go to work.  

> On Dec 13, 2013, at 2:13 PM, Nancy Collins  wrote:
> 
> Hello DART-Users,
> 
> We are very happy to announce the "Lanai" release of DART.
> 
> The full list of new things in the release can be found here:
> 
>  http://www.image.ucar.edu/DAReS/DART/Lanai_release.html#NewFeatures
> 
> One of the notable new features for this release, besides supporting
> a lot of new observation types, new diagnostics and utilities, is support
> for several new models including components of the CESM climate model.
> 
> To download the new version, go to our web page here:
> 
>  http://www2.image.ucar.edu/forms/dart-software-download
> 
> After filling in your contact information you will get the subversion
> links to download the released code.
> 
> The extensive collection of DART web pages can be accessed
> starting here:
> 
>  http://www.image.ucar.edu/DAReS/DART
> 
> Please contact us using  dart at ucar dot edu  to ask questions
> or to report problems.
> 
> Thanks,
> The Entire DART Team
> 
> 
> _______________________________________________
> Dart-users mailing list
> Dart-users at mailman.ucar.edu
> http://mailman.ucar.edu/mailman/listinfo/dart-users

From nancy at ucar.edu  Tue Dec 17 16:46:53 2013
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Tue, 17 Dec 2013 16:46:53 -0700
Subject: [Dart-dev] [6685] DART/trunk/models: update the outlier_threshold
 for lorenz 96, to make it -1 again; 
Message-ID: 

Revision: 6685
Author:   nancy
Date:     2013-12-17 16:46:52 -0700 (Tue, 17 Dec 2013)
Log Message:
-----------
update the outlier_threshold for lorenz 96, to make it -1 again;
and for several of the larger models which generally use real
observations, set it to 3.0 as the suggested default.

Modified Paths:
--------------
    DART/trunk/models/MITgcm_ocean/work/input.nml
    DART/trunk/models/NAAPS/work/input.nml
    DART/trunk/models/clm/work/input.nml
    DART/trunk/models/lorenz_96/work/input.nml
    DART/trunk/models/lorenz_96/work/input.workshop.nml
    DART/trunk/models/mpas_atm/work/input.nml
    DART/trunk/models/mpas_ocn/work/input.nml
    DART/trunk/models/noah/work/input.nml
    DART/trunk/models/rose/work/input.nml
    DART/trunk/models/tiegcm/work/input.nml
    DART/trunk/models/wrf/work/input.nml

-------------- next part --------------
Modified: DART/trunk/models/MITgcm_ocean/work/input.nml
===================================================================
--- DART/trunk/models/MITgcm_ocean/work/input.nml	2013-12-17 18:57:07 UTC (rev 6684)
+++ DART/trunk/models/MITgcm_ocean/work/input.nml	2013-12-17 23:46:52 UTC (rev 6685)
@@ -42,7 +42,7 @@
    output_interval          = 1,
    num_groups               = 1,
    input_qc_threshold       =  3.0,
-   outlier_threshold        = -1.0,
+   outlier_threshold        =  3.0,
    output_forward_op_errors = .false.,
    output_timestamps        = .false.,
    output_inflation         = .true.,

Modified: DART/trunk/models/NAAPS/work/input.nml
===================================================================
--- DART/trunk/models/NAAPS/work/input.nml	2013-12-17 18:57:07 UTC (rev 6684)
+++ DART/trunk/models/NAAPS/work/input.nml	2013-12-17 23:46:52 UTC (rev 6685)
@@ -157,7 +157,7 @@
    output_interval          = 1,
    num_groups               = 1,
    input_qc_threshold       =  3.0,
-   outlier_threshold        = -1.0,
+   outlier_threshold        =  3.0,
    output_forward_op_errors = .false.,
    output_restart_mean      = .false.,
    output_timestamps        = .false.,

Modified: DART/trunk/models/clm/work/input.nml
===================================================================
--- DART/trunk/models/clm/work/input.nml	2013-12-17 18:57:07 UTC (rev 6684)
+++ DART/trunk/models/clm/work/input.nml	2013-12-17 23:46:52 UTC (rev 6685)
@@ -42,8 +42,8 @@
    num_output_obs_members   = 20,
    output_interval          = 1,
    num_groups               = 1,
-   input_qc_threshold       =  1.0,
-   outlier_threshold        =  -1.0,
+   input_qc_threshold       = 1.0,
+   outlier_threshold        = 3.0,
    output_forward_op_errors = .false.,
    output_timestamps        = .false.,
    output_inflation         = .true.,

Modified: DART/trunk/models/lorenz_96/work/input.nml
===================================================================
--- DART/trunk/models/lorenz_96/work/input.nml	2013-12-17 18:57:07 UTC (rev 6684)
+++ DART/trunk/models/lorenz_96/work/input.nml	2013-12-17 23:46:52 UTC (rev 6685)
@@ -42,7 +42,7 @@
    output_interval          = 1,
    num_groups               = 1,
    input_qc_threshold       =  3.0,
-   outlier_threshold        =  3.0,
+   outlier_threshold        = -1.0,
    enable_special_outlier_code = .false.,
    output_forward_op_errors = .false.,
    output_inflation         = .true.,
@@ -78,10 +78,6 @@
    single_restart_file_in  = .true.,
    single_restart_file_out = .true.,
    perturbation_amplitude  = 0.2,
-   flag_unneeded_transposes = .true.
-   layout = 1,
-   communication_configuration = 1,
-   debug = .false.,
    /
 
 &assim_tools_nml
@@ -143,7 +139,7 @@
    /
 
 &preprocess_nml
-          overwrite_output = .true.
+          overwrite_output = .true.,
     input_obs_def_mod_file = '../../../obs_def/DEFAULT_obs_def_mod.F90',
    output_obs_def_mod_file = '../../../obs_def/obs_def_mod.f90',
    input_obs_kind_mod_file = '../../../obs_kind/DEFAULT_obs_kind_mod.F90',

Modified: DART/trunk/models/lorenz_96/work/input.workshop.nml
===================================================================
--- DART/trunk/models/lorenz_96/work/input.workshop.nml	2013-12-17 18:57:07 UTC (rev 6684)
+++ DART/trunk/models/lorenz_96/work/input.workshop.nml	2013-12-17 23:46:52 UTC (rev 6685)
@@ -13,7 +13,7 @@
    restart_out_file_name    = "perfect_restart",
    obs_seq_in_file_name     = "obs_seq.in",
    obs_seq_out_file_name    = "obs_seq.out",
-   adv_ens_command          = "./advance_model.csh",
+   adv_ens_command          = "../shell_scripts/advance_model.csh",
    trace_execution          = .false.,
    output_timestamps        = .false.,
    print_every_nth_obs      = -1,
@@ -23,7 +23,7 @@
 
 &filter_nml
    async                    = 0,
-   adv_ens_command          = "./advance_model.csh",
+   adv_ens_command          = "../shell_scripts/advance_model.csh",
    ens_size                 = 20,
    start_from_restart       = .true.,
    output_restart           = .true.,
@@ -43,6 +43,7 @@
    num_groups               = 1,
    input_qc_threshold       =  3.0,
    outlier_threshold        = -1.0,
+   enable_special_outlier_code = .false.,
    output_forward_op_errors = .false.,
    output_inflation         = .true.,
    output_timestamps        = .false.,
@@ -168,9 +169,9 @@
    /
 
 &obs_sequence_tool_nml
-   filename_seq      = 'obs_seq.final',
+   filename_seq      = 'obs1.out', 'obs2.out',
    filename_seq_list = '',
-   filename_out      = 'obs_seq.processed',
+   filename_out      = 'obs_seq.combined',
    first_obs_days    = -1,
    first_obs_seconds = -1,
    last_obs_days     = -1,
@@ -206,7 +207,7 @@
    obs_sequence_name     = 'obs_seq.final',
    bin_width_days        = -1,
    bin_width_seconds     = -1,
-   init_skip_days        = 0,
+   init_skip_days        = 0, 
    init_skip_seconds     = 0,
    Nregions              = 3,
    trusted_obs           = 'null',

Modified: DART/trunk/models/mpas_atm/work/input.nml
===================================================================
--- DART/trunk/models/mpas_atm/work/input.nml	2013-12-17 18:57:07 UTC (rev 6684)
+++ DART/trunk/models/mpas_atm/work/input.nml	2013-12-17 23:46:52 UTC (rev 6685)
@@ -42,7 +42,7 @@
    output_interval          = 1,
    num_groups               = 1,
    input_qc_threshold       =  3.0,
-   outlier_threshold        = -1.0,
+   outlier_threshold        =  3.0,
    output_forward_op_errors = .true.,
    output_timestamps        = .false.,
    output_inflation         = .true.,

Modified: DART/trunk/models/mpas_ocn/work/input.nml
===================================================================
--- DART/trunk/models/mpas_ocn/work/input.nml	2013-12-17 18:57:07 UTC (rev 6684)
+++ DART/trunk/models/mpas_ocn/work/input.nml	2013-12-17 23:46:52 UTC (rev 6685)
@@ -42,7 +42,7 @@
    output_interval          = 1,
    num_groups               = 1,
    input_qc_threshold       =  3.0,
-   outlier_threshold        = -1.0,
+   outlier_threshold        =  3.0,
    output_forward_op_errors = .false.,
    output_timestamps        = .false.,
    output_inflation         = .true.,

Modified: DART/trunk/models/noah/work/input.nml
===================================================================
--- DART/trunk/models/noah/work/input.nml	2013-12-17 18:57:07 UTC (rev 6684)
+++ DART/trunk/models/noah/work/input.nml	2013-12-17 23:46:52 UTC (rev 6685)
@@ -73,7 +73,7 @@
    output_interval          = 1,
    num_groups               = 1,
    input_qc_threshold       =  3.0,
-   outlier_threshold        = -1.0,
+   outlier_threshold        =  3.0,
    output_forward_op_errors = .false.,
    output_timestamps        = .false.,
    output_inflation         = .true.,

Modified: DART/trunk/models/rose/work/input.nml
===================================================================
--- DART/trunk/models/rose/work/input.nml	2013-12-17 18:57:07 UTC (rev 6684)
+++ DART/trunk/models/rose/work/input.nml	2013-12-17 23:46:52 UTC (rev 6685)
@@ -42,7 +42,7 @@
    output_interval          = 1,
    num_groups               = 1,
    input_qc_threshold       =  3.0,
-   outlier_threshold        = -1.0,
+   outlier_threshold        =  3.0,
    output_forward_op_errors = .false.,
    output_timestamps        = .false.,
    output_inflation         = .true.,

Modified: DART/trunk/models/tiegcm/work/input.nml
===================================================================
--- DART/trunk/models/tiegcm/work/input.nml	2013-12-17 18:57:07 UTC (rev 6684)
+++ DART/trunk/models/tiegcm/work/input.nml	2013-12-17 23:46:52 UTC (rev 6685)
@@ -42,7 +42,7 @@
    output_interval          = 1,
    num_groups               = 1,
    input_qc_threshold       =  3.0,
-   outlier_threshold        = -1.0,
+   outlier_threshold        =  3.0,
    output_forward_op_errors = .false.,
    output_timestamps        = .false.,
    output_inflation         = .true.,

Modified: DART/trunk/models/wrf/work/input.nml
===================================================================
--- DART/trunk/models/wrf/work/input.nml	2013-12-17 18:57:07 UTC (rev 6684)
+++ DART/trunk/models/wrf/work/input.nml	2013-12-17 23:46:52 UTC (rev 6685)
@@ -42,7 +42,7 @@
    output_interval          = 1,
    num_groups               = 1,
    input_qc_threshold       =  3.0,
-   outlier_threshold        = -1.0,
+   outlier_threshold        =  3.0,
    output_forward_op_errors = .false.,
    output_timestamps        = .false.,
    output_inflation         = .true.,

From nancy at ucar.edu  Wed Dec 18 10:18:11 2013
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Wed, 18 Dec 2013 10:18:11 -0700
Subject: [Dart-dev] [6688] DART/trunk/models/gitm/work/pbs_file.sh:
	Replacing a corrupt file.
Message-ID: 

Revision: 6688
Author:   thoar
Date:     2013-12-18 10:18:10 -0700 (Wed, 18 Dec 2013)
Log Message:
-----------
Replacing a corrupt file. The file that got committed was the result
of using a patchfile ... twice. The second time the patch command was run,
it appended an identical version of the script onto the existing version.
Basically, I just removed HALF the file of the original commit.

Modified Paths:
--------------
    DART/trunk/models/gitm/work/pbs_file.sh

-------------- next part --------------
Modified: DART/trunk/models/gitm/work/pbs_file.sh
===================================================================
--- DART/trunk/models/gitm/work/pbs_file.sh	2013-12-18 16:25:42 UTC (rev 6687)
+++ DART/trunk/models/gitm/work/pbs_file.sh	2013-12-18 17:18:10 UTC (rev 6688)
@@ -166,171 +166,3 @@
 ./obs_diag > obs_diag.out || exit 8
 
 echo 'pbs_file.sh: past-od' `date`
-#!/bin/bash
-#PBS -S /bin/bash
-#PBS -N dart_test_tec
-#PBS -l procs=21,pmem=1000mb,walltime=1:00:00
-#PBS -A ACCOUNT
-#PBS -l qos=ACCOUNT
-#PBS -q QUE
-#PBS -M USERNAME at EXAMPLE.com
-#PBS -m abe
-#PBS -V
-
-#No semicolons after numerical values please, and a space before comments (this file is read into matlab, so certain rules have to be followed) also no / in the end of paths as I add them later
-hd=~/HEAD/DART/models/gitm #directory where gitm is located
-rd=/nobackup/NYXUSERNAME #temporary directory where you want to run the simulation on
-noe=20 #number of ensemble members
-nop=1 #number of processors per member
-
-prs=1        #do you want to prespin? 1=yes, 0=no. Note, if you say no, it will assume you have "prespun" directories already available in folder specified on line 160ish below, so default, do Yes=1, even for short period of time just to get the folder structure in place (to adjust the length of prespin, change $hd copy of gitm/GITM2/srcData/UAM.in.test.DART.time_prespin ) 
-ts=1         #do you want to do a "Truth Spin"? Yes = 1, no = 0. Not necessary for anything but plotting and generating "truth data" for later runs (so setting it to 0 is ok for initial tests).
-est_f107=1   #do you want to estimate f107? 0=no, 1=yes. If you don't estimate f107, it is just kept constant at whatever it was initialized in clean.sh (will overwrite a line in the $hd of model_mod.f90 before building)
-nbn=2        #Number of Blocks loNgitude (if bui=1, will overwrite a line in the $hd copy of gitm/GITM2/srcData/UAM.in.test.DART.data_ens and gitm/GITM2/srcData/UAM.in.test.DART.data_truth)
-nbt=2        #Number of Blocks laTitude (see line before) 
-ncn=9        #Number of Cells in each block in loNgitude (if bui=1, will overwrite a line in the $hd copy of gitm/GITM2/src/ModSize.f90)
-nct=9        #Number of Cells in each block in laTitude (if bui=1, will overwrite a line in the $hd copy of gitm/GITM2/src/ModSize.f90)
-nca=50       #Number of Cells in Altgitude (no block division in alt) (if bui=1, will overwrite a line in the $hd copy of gitm/GITM2/src/ModSize.f90)
-bui=0        #do you want this script to re-make GITM and re-make DART? Yes = 1, no = 0. Do 0, unless you changed some code or $est_f107 or $nbn, etc above.
-f1t=150.0    #if you set $ts=1 above, what f107 would you like to use in that run (gets fed into clean.sh below). If you would like to use a real f107 (from f107.txt), uncomment lines 61 and 62 in clean.sh
-f1m=150.0    #to do assimilation, you need to create an ensemble. The way it has been done so far is by creating several GITM instances with different f107's (sampled from normal distribution). What would you like the mean of f107 initial distribution to be? (gets fed to clean.sh below)
-f1s=5.0      #what would you like the standard deviation of the initial distribution for f107 to be?
-cfh=0.6      #horizontal cutoff, ie half-width of a Gaspari-Cohn polinomial for localizing observations, measured in horizontal great circle radians (not just latitude and longitude!). See section 8 of DART tutorial, slide 14 and cov_cutoff_mod.f90:line 142, and Gaspari and Cohn, 1999, QJRMS, eq 4.10 (will overwrite a line in the $rd copy of input.nml)
-cfv=100000   #vert_normalization_height - like horizontal cutoff, but in vertical dimension, half-width of a Gaspari-Cohn polinomial. Measured in meters (will overwrite a line in the $rd copy of input.nml)
-inf_v=1.01   #whole state inflation value - lambda on slide 6 of section 9 of DART tutorial and \lambda in eq (16) in gitm/GITM2/srcDoc/thermo.pdf and .tex and \gamma in Anderson and Anderson 1999 "A Monte Carlo Implementation of the Nonlinear Filtering Problem ...". This is a scaling up, so 1.01 corresponds to 1 percent increase over old values, 1.24 would be a 24% increase, etc. (will overwrite a line in the $rd copy of input.nml)
-pr=1.0       #driver inflation value - constant variance of the driver as denoted by \sigma_i^2 in eq (18) in gitm/GITM2/srcDoc/thermo.pdf and .tex, measured in SFU^2 (will be communicated to GITM via sigma_i2.txt below, read into GITM in restart.f90)
-aw=1800      #assimilation_period_seconds - ammount of simulated time between producing DART prior and posterior estimates, which requires GITM restarts, so making this period smaller will slow down the runs as writing GITM restarts takes time (will overwrite a line in the $rd copy of input.nml)
-awt=300.0    #period between writing 3DALL/3DUSR files for the truth simulation (will overwrite line(s) in the $hd GITM2/srcData/UAM.in.test.DART.data_truth)
-fk=1         #filter_kind in input.nml - see section 6 in DART tutorial - 1=EAKF, 2=EnKF, 3=Kernel, 4=particle, 5=rand samp, 6=kurtosis, 7=box kernel (will overwrite a line in the $rd copy of input.nml)
-
-if [ $bui -eq 1 ]; then
-    cd $hd/work
-    cd ../GITM2
-#change ModSize.f90 (GITM grid-size file)
-    sed -i'.tmp' 's/  integer, parameter :: nLons =.*/  integer, parameter :: nLons ='$ncn'/' src/ModSize.f90
-    sed -i'.tmp' 's/  integer, parameter :: nLats =.*/  integer, parameter :: nLats ='$nct'/' src/ModSize.f90
-    sed -i'.tmp' 's/  integer, parameter :: nAlts =.*/  integer, parameter :: nAlts ='$nca'/' src/ModSize.f90
-#change UAM.in (GITM input file) 
-    sed -i'.tmp' 's/.*lons/'$nbn'    lons/' srcData/UAM.in.test.DART.data_ens
-    sed -i'.tmp' 's/.*lats/'$nbt'    lats/' srcData/UAM.in.test.DART.data_ens
-    sed -i'.tmp' 's/.*lons/'$nbn'    lons/' srcData/UAM.in.test.DART.data_truth
-    sed -i'.tmp' 's/.*lats/'$nbt'    lats/' srcData/UAM.in.test.DART.data_truth
-    sed -i'.tmp' 's/.*dt for output/'$awt'    dt for output/' srcData/UAM.in.test.DART.data_truth
-
-    make || exit 1 
-
-
-    cd ../work
-    if [ $est_f107 -eq 0 ]; then #don't estimate f107
-	sed -i'.tmp' 's/dist(k) =.*!changed.*/dist(k) = 1000.0 !changed by pbs_file script/' ../model_mod.f90 #every obs is very far away from f107 location (1000 radians is beyond physically meaningful 2pi radians on a sphere)
-    else #estimate f107
-	sed -i'.tmp' 's/dist(k) =.*!changed.*/dist(k) = 0 !changed by pbs_file script/' ../model_mod.f90 #every obs is exactly very close to the f107 location
-    fi
-    ./quickbuild.csh  || exit 2
-fi
-
-echo 'pbs_file.sh: start' `date` 
-
-rm -rf $rd/${PBS_JOBNAME} #DELETES THE OLD DIRECTORY!
-mkdir $rd/${PBS_JOBNAME} || exit 3 #makes a new directory on nobackup using the name of this job
-cd $rd/${PBS_JOBNAME} 
-cp -r $hd . || exit 4
-cd gitm/work || exit 5
-
-echo 'pbs_file.sh: past-cp' `date`
-
-#change advance_model.csh to have the right number of processes
-sed -i'.tmp' 's/@ nop = .* #changed.*/@ nop = '$nop' #changed by pbs_file script/' ../shell_scripts/advance_model.csh
-
-#change input.nml (DART input file)
-sed -i'.tmp' 's/ens_size.*=.*/ens_size = '$noe',/' input.nml   
-sed -i'.tmp' 's/cutoff.*=.*/cutoff = '$cfh',/' input.nml
-sed -i'.tmp' 's/vert_normalization_height.*=.*/vert_normalization_height = '$cfv',/' input.nml
-sed -i'.tmp' 's/assimilation_period_seconds.*=.*/assimilation_period_seconds  = '$aw',/' input.nml
-sed -i'.tmp' 's/filter_kind.*=.*/filter_kind = '$fk',/' input.nml
-sed -i'.tmp' 's/inf_initial = 1.10, 1.0,/inf_initial = '$inf_v', 1.0,/' input.nml   
-
-#choose the observations file
-cp obs_seq.out.TEC obs_seq.out #TEC
-#cp obs_seq.out.CHAMP obs_seq.out #CHAMP
-
-pre=prespin_ #prefix for copies of prespinned folders
-
-if [ $prs -eq 1 ]; then #make new prespin
-
-    (./clean.sh $noe $nop $ts $f1t $f1m $f1s  >& output_c) || exit 5    
-    for (( i = 1 ; i <= $[$noe + $ts]; i++ )) 
-    do
-	if [ $est_f107 -eq 0 ] ; then #don't estimate f107, so no need to inflate it, so keep the #DART=0 in all UAM.in's, nothing to change
-	    cp -R advance_temp_e$i ${pre}advance_temp_e$i  #save a copy of the prespun directories
-	else #estimate f107, so change #DART=0 flags in UAM.in's to appropriate settings:
-	    
-	    if [ $i -eq 1 ] ; then #first ens member is the master (1)
-		sed -i'' 's/.*useDART (0=no, 1=master, 2=slave)/1  useDART (0=no, 1=master, 2=slave)/' advance_temp_e$i/UAM.in.truncated
-		echo $noe > advance_temp_e$i/ens_size.txt
-		echo $pr > advance_temp_e$i/sigma_i2.txt		
-	    elif [ $i -eq $[$noe+1] ] ; then #truth is noe+1 (and no need for DART, hence 0)
-		sed -i'' 's/.*useDART (0=no, 1=master, 2=slave)/0  useDART (0=no, 1=master, 2=slave)/' advance_temp_e$i/UAM.in.truncated   
-	    else #other ens members are slaves (2)
-		sed -i'' 's/.*useDART (0=no, 1=master, 2=slave)/2  useDART (0=no, 1=master, 2=slave)/' advance_temp_e$i/UAM.in.truncated
-	    fi
-	    
-	    cp -R advance_temp_e$i ${pre}advance_temp_e$i #save a copy of the prespun directories
-
-	fi
-    done
-    
-else #prespin already exists
-    
-    ps=$rd/dart_test_ch/gitm/work #if you have already prespun the ensmble in one of the previous runs, tell me where it is
-    
-    cp ${ps}/perfect_ics . #only needed if you use perfect_model_obs
-    cp ${ps}/filter_ics.* .
-    for (( i = 1 ; i <= $[$noe + $ts]; i++ )) 
-    do
-	cp -r ${ps}/${pre}advance_temp_e$i advance_temp_e$i #copy the old prespin here and remove the prefix
-	if [ $est_f107 -eq 0 ] ; then #don't estimate f107
-	    echo ' ' #don't spread f107 means don't do anything as the prespin already had #DART=0
-	else #estimate f107
-	    if [ $i -eq 1 ] ; then #first ens member is the master (1)
-		sed -i'' 's/.*useDART (0=no, 1=master, 2=slave)/1  useDART (0=no, 1=master, 2=slave)/' advance_temp_e$i/UAM.in.truncated
-		echo $noe > advance_temp_e$i/ens_size.txt
-		echo $pr > advance_temp_e$i/sigma_i2.txt		
-	    elif [ $i -eq $[$noe+1] ] ; then #truth is noe+1 (and no need for DART, hence 0)
-		sed -i'' 's/.*useDART (0=no, 1=master, 2=slave)/0  useDART (0=no, 1=master, 2=slave)/' advance_temp_e$i/UAM.in.truncated   
-	    else #other ens members are slaves (2)
-		sed -i'' 's/.*useDART (0=no, 1=master, 2=slave)/2  useDART (0=no, 1=master, 2=slave)/' advance_temp_e$i/UAM.in.truncated
-	    fi  
-	fi
-    done    
-fi
-
-echo 'pbs_file.sh: past-ps' `date`
-
-if [ $ts -eq 1 ]; then #if you requested a "truth spin"
-#./run_p_fv.bash $noe $nop $vv || echo 1 POM fail  #the traditional DART way of doing it
-    cd advance_temp_e$[$noe+1]
-    cat ../../GITM2/srcData/UAM.in.test.DART.time_truth UAM.in > UAM.in.temporary #combine the data and time parts 
-    mv UAM.in.temporary UAM.in
-    echo " "             >> UAM.in 
-    echo "#END"          >> UAM.in
-    rm restartIN #remove symbolic link to restartOUT.out (where DART puts its restarts for GITM)
-    rm UA/restartIN
-    ln -s UA/restartOUT restartIN # and instead link it to the GITM's native restart location (restartOUT)
-    ln -s restartOUT UA/restartIN
-
-    tail -n $nop $PBS_NODEFILE > hf #create the hostfile for truth
-    cat hf
-    ( mpiexec -hostfile hf -n $nop GITM.exe < /dev/null > ens_log.txt ) & #run truth simulation on hf in background
-    cd .. 
-fi
-
-echo 'pbs_file.sh: past-ts' `date`
-
-(./run_f.bash $noe $[$noe*$nop] > output_f ) || exit 7 #nyx
-
-echo 'pbs_file.sh: past-f' `date`
-
-./obs_diag > obs_diag.out || exit 8
-
-echo 'pbs_file.sh: past-od' `date`

From nancy at ucar.edu  Tue Dec 31 11:55:23 2013
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Tue, 31 Dec 2013 11:55:23 -0700
Subject: [Dart-dev] [6706] DART/trunk/models/mpas_atm/model_mod.f90: if the
 get_close_obs() routine has to do a vertical conversion
Message-ID: 

Revision: 6706
Author:   nancy
Date:     2013-12-31 11:55:22 -0700 (Tue, 31 Dec 2013)
Log Message:
-----------
if the get_close_obs() routine has to do a vertical conversion
for vertical localization, have it store the converted location
in the list that gets passed back to filter.  with this single-line
change, each observation which is close to other obs will only
have to do a vertical conversion once instead of multiple times.
this change was tested by so-young and produced identical results
with a faster running speed.

Modified Paths:
--------------
    DART/trunk/models/mpas_atm/model_mod.f90

-------------- next part --------------
Modified: DART/trunk/models/mpas_atm/model_mod.f90
===================================================================
--- DART/trunk/models/mpas_atm/model_mod.f90	2013-12-30 21:22:40 UTC (rev 6705)
+++ DART/trunk/models/mpas_atm/model_mod.f90	2013-12-31 18:55:22 UTC (rev 6706)
@@ -2043,11 +2043,11 @@
   else if (base_which /= vert_localization_coord) then
       call vert_convert(ens_mean, base_obs_loc, base_obs_kind, ztypeout, istatus1)
       if(debug > 5) then
-      call write_location(0,base_obs_loc,charstring=string1)
-      call error_handler(E_MSG, 'get_close_obs: base_obs_loc',string1,source, revision, revdate)
-  endif
+         call write_location(0,base_obs_loc,charstring=string1)
+         call error_handler(E_MSG, 'get_close_obs: base_obs_loc',string1,source, revision, revdate)
+     endif
+   endif
 endif
-endif
 
 if (istatus1 == 0) then
 
@@ -2070,6 +2070,7 @@
       if (.not. horiz_dist_only) then
           if (local_obs_which /= vert_localization_coord) then
               call vert_convert(ens_mean, local_obs_loc, obs_kind(t_ind), ztypeout, istatus2)
+              obs_loc(t_ind) = local_obs_loc
           else
               istatus2 = 0
           endif

From nancy at ucar.edu  Tue Dec 31 11:56:16 2013
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Tue, 31 Dec 2013 11:56:16 -0700
Subject: [Dart-dev] [6707] DART/trunk/doc/html/Lanai_release.html: update
 the part of the release notes that describe the
Message-ID: 

Revision: 6707
Author:   nancy
Date:     2013-12-31 11:56:16 -0700 (Tue, 31 Dec 2013)
Log Message:
-----------
update the part of the release notes that describe the
matlab toolboxes which are needed.  the 'netcdf_toolbox'
is no longer needed.

Modified Paths:
--------------
    DART/trunk/doc/html/Lanai_release.html

-------------- next part --------------
Modified: DART/trunk/doc/html/Lanai_release.html
===================================================================
--- DART/trunk/doc/html/Lanai_release.html	2013-12-31 18:55:22 UTC (rev 6706)
+++ DART/trunk/doc/html/Lanai_release.html	2013-12-31 18:56:16 UTC (rev 6707)
@@ -1695,27 +1695,24 @@
 
[top]

 
 Matlab® Diagnostics
-The output files are netCDF files, and may be examined with many
-different software packages. We happen to use Matlab®, and provide our
+
The output files are netCDF files and may be examined with many
+different software packages. We use Matlab®, and provide our
 diagnostic scripts in the hopes that they are useful.
 
 
 The diagnostic scripts and underlying functions reside in two places: 
 DART/diagnostics/matlab and
-DART/matlab. They are reliant on the public-domain 
-
-netcdf toolbox from 
-http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html
-as well as the public-domain 
-CSIRO matlab/netCDF interface
-from http://www.marine.csiro.au/sw/matlab-netcdf.html.
+DART/matlab. 
+They are reliant on the public-domain MEXNC/SNCTOOLS netCDF interface from
+http://mexcdf.sourceforge.net.
 If you do not have them installed on your system and want to use Matlab to peruse netCDF,
 you must follow their installation instructions. The 'interested reader' may want to
 look at the DART/matlab/startup.m file I use on my system.
-If you put it in your $HOME/matlab directory, it is invoked every time you start up Matlab.
+If you put it in your $HOME/matlab directory 
+it is invoked every time you start up Matlab.
 
 
-Once you can access the getnc function from within Matlab,
+
Once you can access the nc_varget function from within Matlab
 you can use our diagnostic scripts. It is necessary to prepend the location of
 the DART/matlab scripts to the matlabpath. 
 Keep in mind the location of the netcdf
@@ -1739,8 +1736,8 @@
   To get started, type one of these: helpwin, helpdesk, or demo.
   For product information, visit www.mathworks.com.
 
->> which getnc
-/contrib/matlab/matlab_netcdf_5_0/getnc.m
+>> which nc_varget
+/contrib/matlab/snctools/4024/nc_varget.m
 >>ls *.nc
 
 ans =

set_def.out # Output file name

hardware	O/S	F90 compiler	batch manager/mpi
Intel cluster/SMP/32 bit	Red Hat Enterprise	Intel 9.0 (build 20051201)	none
Intel cluster/SMP/32 bit	Red Hat Enterprise	GNU Fortran 95 4.1.0	none
Intel Nocona	SUSE	PGI 6.0-8	LSF
Intel Nocona	SUSE	Intel 9.1 (EM64T)	LSF
Intel iMac	Mac OS X 10.4.6	gfortran 4.2.0	Open-MPI
IBM Power 5+	AIX 5.3	XLF 12.1.0	LSF
Intel	Fedora Core 4	Intel 9.0	none
Macbook Pro (Intel)	Mac OS X 10.6.8	Intel F90 11.1	OpenMPI
Macbook Pro (Intel)	Mac OS X 10.6.8	gfortran 4.5.2	OpenMPI
PowerBook G4 (PowerPC)	Mac OS X 10.4.8	Absoft Pro Fortran 9.0	none
PowerBook G4 (PowerPC)	Mac OS X 10.3.9	Absoft Pro Fortran 9.0	Lam
PowerBook G4 (PowerPC)	Mac OS X 10.3.9	gfortran 4.2.0	Lam
Intel cluster (Xeon)	Fedora Core 2	PGI 6.0-5	PBS
Intel cluster (Xeon)	Fedora Core 2	PGI 5.2-4	PBS
Intel cluster (Xeon)	Fedora Core 2	Lahey 6.20c	PBS
IBM cluster (of opterons)	SUSE Enterprise 8	Pathscale 2.4	LSF
IBM cluster (of opterons)	Suse Enterprise 8	Intel 9.1 (EM64T)	LSF
IBM cluster (of opterons)	Suse Enterprise 8	PGI 6.2	LSF
SGI Altix	SUSE Linux ES 9.3	Intel 9.1	PBS
SGI MIPS	IRIX 6.5	MIPSpro 7.4.3m	NQS
Linux cluster	Intel	Intel 11.1	PBS

Contact:	Tim Hoar
Revision:	$Revision$
Source:	$URL$
Change Date:	$Date$
Change history:	try "svn log" or "svn diff"

Contact:	Tim Hoar
Revision:	$Revision$
Source:	$URL$
Change Date:	$Date$
Change history:	try "svn log" or "svn diff"

namelist variable	description
async	Simply ignore this. Leave it set to '.false.'
obs_seq_in_file_name	specifies the file name that results from running - create_obs_sequence, i.e. the - 'observation sequence definition' file.
obs_seq_out_file_name	specifies the output file name containing the - 'observation sequence', finally populated with - (perfect?) 'observations'.
start_from_restart	When set to 'false', - perfect_model_obs generates an - arbitrary initial condition (which cannot be guaranteed - to be on the L63 attractor).
output_restart	When set to 'true', - perfect_model_obs will record - the model state at the end of this integration in the file - named by restart_out_file_name.
restart_in_file_name	is ignored when 'start_from_restart' is 'false'.
restart_out_file_name	if output_restart is 'true', - this specifies the name of the file containing the model - state at the end of the integration.
init_time_xxxx	the start time of the integration.
output_interval	interval at which to save the model state.

Contents	Type	Description
dart_to_gitm_output_file	character(len=128)	The name of the DART file containing the model state + derived from the GITM restart files.
advance_time_present	logical	If you are manually converting a DART initial conditions or + restart file this should be .false.; these files have + a single timestamp describing the valid time of the model state. + If .true., TWO timestamps are expected in the DART + file header and DART_GITM_time_control.txt) is created with + the settings appropriate to advance GITM to the time requested by DART.

Contents	Type	Description
gitm_restart_dirname	character(len=256)	The name of the directory containing the + GITM restart files and runtime control information.
gitm_state_variables	character(len=32), + dimension(2,80)	The list of variable names in the gitm restart file to use to + create the DART state vector and their corresponding DART kind. + The default list is specified in + model_mod.nml

Item	Type	Description
model_analysis_filename	character(len=256) + [default: 'mpas_init.nc']	The name of the MPAS analysis file to be read and/or written + by the DART programs for the state data.
grid_definition_filename	character(len=256) + [default: 'mpas_init.nc']	The name of the MPAS file to be read + by the DART programs for the grid information. Generally + this is the same as the model_analysis_filename. + However, the grid information is large and if the grid is static + that information could be omitted from the analysis files to + save space. A single grid file could be supplied once and + not change during the assimilation run.
highest_obs_pressure_mb	real(r8) + [default: 100.0]	Observations higher than this pressure are ignored. Set to -1.0 + to ignore this test. For models with a prescribed top boundary + layer, trying to assimilate very high observations results in + problems because the model damps out any changes the assimilation + tries to make. With adaptive algorithms this results in larger + and larger coefficients as the assimilation tries to effect state + vector change. +
output_state_vector	logical [default: .false.]	The switch to determine the form of the state vector in the + output netCDF files. If .true. + the state vector will be output exactly as DART uses it; + as one long array. If .false., + the state vector is parsed into prognostic variables and + output that way -- much easier to use with 'ncview', for + example. [Recommended]
assimilation_period_days	integer [default: 0]	The number of days to advance the model for each assimilation. + Even if the model is being advanced outside of the DART filter + program, the assimilation period should be set correctly. + Only observations with a time within +/- 1/2 this window size + will be assimilated. +
assimilation_period_seconds	integer [default: 21600]	In addition to assimilation_period_days, + the number of seconds to advance the model for each assimilation.
vert_localization_coord	integer [default: 3]	Vertical coordinate for vertical localization. + + 1 = model level + 2 = pressure (in pascals) + 3 = height (in meters) + 4 = scale height (unitless) +
sfc_elev_max_diff	real(r8)[default: -1.0]	If > 0, the maximum difference, in meters, between an observation marked + as a 'surface obs' as the vertical type (with the surface elevation, in + meters, as the numerical vertical location), and the surface elevation as + defined by the model. Observations further away from the surface than this + threshold are rejected and not assimilated. If the value is negative, this + test is skipped.
log_p_vert_interp	logical [default: .true.]	If .true., vertical interpolation is done in log-pressure. Otherwise, linear.
use_u_for_wind	logical [default: .false.]	If .false., zonal and meridional winds at cell centers are used for + the wind observation operator [default]. In that case, triangular meshes are used for the + barycentric (e.g., area-weighted) interpolation. If .true., wind vectors at an arbitrary + (e.g., observation) point are reconstructed from the normal component of velocity on cell edges + (u) using radial basis functions (RBFs) provided by the MPAS model.
use_rbf_option	integer [default: 2]	If use_u_for_wind is .true., this option controls + how many points will be used in the RBF interpolation. Options are available as 1, 2, and 3. + All the edges available in N (= 1,2, or 3) cells go into the RBF reconstruction.
update_u_from_reconstruct	logical [default: .true.]	When zonal and meridional winds at cell centers are used for + the wind observation operator (use_u_for_wind = .false.), + this option decides if the normal component of velocity on cell edges (which is + the only wind prognostic variable in MPAS-ATM) should be updated from the winds at cell centers. + If .true., use_increments_for_u_update should be also decided. + If use_u_for_wind = .true. and the normal component of velocity on cell + edges is defined as a state vector, this option should be .false. so the edge winds can be + directly updated by filter.
use_increments_for_u_update	logical [default: .true.]	Only if update_u_from_reconstruct is .true., this option is + used to decide if the edge winds are replaced by averaging from the analysis + winds at cell centers (.false.), or just updated by the analysis increments + at cell centers (.true.). If .true., all the wind components (e.g., both at + cell centers and edges) are read from prior and used to compute the + increments [Recommended].
model_perturbation_amplitude	real(r8) [default: 0.0001]	The amplitude of random noise to add when trying to perturb a single + state vector to create an ensemble. Only used when + input.nml::&filter_nml:start_from_restart = .false. + + Multiplied by the state vector, it produces standard deviation + of a gaussian distribution with the mean at the value of the state vector element.
calendar	character(len=32) + [default: 'Gregorian']	Character string specifying the calendar being used by MPAS.
debug	integer [default: 0]	The switch to specify the run-time verbosity. + 0 is as quiet as it gets. + > 1 provides more run-time messages. + > 5 provides ALL run-time messages. +

Item	Type	Description
mpas_vars_nml	character(len=NF90_MAX_NAME):: + dimension(160) +	The table that relates the MPAS-ATM variables + to use to build the DART state vector, and the corresponding + DART kinds for those variables. The first column in each pair must + be the NetCDF name of a field in the MPAS file. The second column + in each pair must be a KIND known to the DART system. See the + obs_kind/obs_kind_mod.f90 file for known names. + These must be generic kinds, not specific types. +
mpas_state_bounds	character(len=NF90_MAX_NAME):: + dimension(160) +	MPAS-ATM variables that need to set up lower and upper bound values. + Columns are a variable name, min, max values, and 'CLAMP' or 'FAIL' in case + the field goes beyond the bounds. If the bound values have 'NULL', + the actual data range is used.

integer :: nCells	the number of Cell Centers
integer :: nEdges	the number of Cell Edges
integer :: nVertices	the number of Cell Vertices
integer :: nVertLevels	the number of vertical level midpoints
integer :: nVertLevelsP1	the number of vertical level edges
integer :: nSoilLevels	the number of soil level ?midpoints?
real(r8) :: latCell(:)	the latitudes of the Cell Centers (-90,90)
real(r8) :: lonCell(:)	the longitudes of the Cell Centers [0, 360)
real(r8) :: zgrid(:,:)	cell center geometric height at cell centers (ncells,nvert)
integer :: nCells	the number of cell centers
integer :: nEdges	the number of cell edges
integer :: nVertices	the number of cell vertices
integer :: nVertLevels	the number of vertical levels for mass fields
integer :: nVertLevelsP1	the number of vertical levels for vertical velocity
integer :: nSoilLevels	the number of soil levels
real(r8) :: latCell(:)	the latitudes of the cell centers [-90,90]
real(r8) :: lonCell(:)	the longitudes of the cell centers [0, 360]
real(r8) :: latEdge(:)	the latitudes of the edges [-90,90], if edge winds are used.
real(r8) :: lonEdge(:)	the longitudes of the edges [0, 360], if edge winds are used.
real(r8) :: xVertex(:)	The cartesian location in x-axis of the vertex
real(r8) :: yVertex(:)	The cartesian location in y-axis of the vertex
real(r8) :: zVertex(:)	The cartesian location in z-axis of the vertex
real(r8) :: xEdge(:)	The cartesian location in x-axis of the edge, if edge winds are used.
real(r8) :: yEdge(:)	The cartesian location in y-axis of the edge, if edge winds are used.
real(r8) :: zEdge(:)	The cartesian location in z-axis of the edge, if edge winds are used.
real(r8) :: zgrid(:,:)	geometric height at cell centers (nCells, nVertLevelsP1)
integer :: CellsOnVertex(:,:)	list of cell centers defining a triangle
integer :: edgesOnCell(:,:)	list of edges on each cell
integer :: verticesOnCell(:,:)	list of vertices on each cell
integer :: edgeNormalVectors(:,:)	unit direction vectors on the edges (only used if use_u_for_wind = .true.)

Contents	Type	Description
model_analysis_filename	character(len=256) - [default: 'mpas_analysis.nc']	Character string specifying the name of the MPAS analysis - file to be read and/or written by the different program units.
output_state_vector	logical [default: .true.]	The switch to determine the form of the state vector in the - output netCDF files. If .true. - the state vector will be output exactly as DART uses it - ... one long array. If .false., - the state vector is parsed into prognostic variables and - output that way -- much easier to use with 'ncview', for - example.
assimilation_period_days	integer [default: 1]	The number of days to advance the model for each assimilation. -
assimilation_period_seconds	integer [default: 0]	In addition to assimilation_period_days, - the number of seconds to advance the model for each assimilation. -
model_perturbation_amplitude	real(r8) [default: 0.2]	Reserved for future use. -
calendar	character(len=32) - [default: 'Gregorian']	- Character string specifying the calendar being used by MPAS.
debug	integer [default: 0]	The switch to specify the run-time verbosity. - 0 is as quiet as it gets. - > 1 provides more run-time messages. - > 5 provides ALL run-time messages. -

program	purpose
create_obs_set_def	specify a (set) of observation characteristics taken - by a particular (set of) instruments -
create_obs_sequence	specify the temporal attributes of the observation sets -
perfect_model_obs	spinup, generate "true state" for synthetic observation experiments, ... -
filter	perform experiments -

namelist variable	description
ens_size	Number of ensemble members. - 20 is sufficient for most of the exercises.
cutoff	to limit the impact of an observation, set to 0.0 - (i.e. spin-up)
cov_inflate	A value of 1.0 results in no inflation.(spin-up)

Dart Overview

Quick Guide Topics

DART tested platforms/models/compilers

DART platforms/compilers/batch systems

DART code distributions

Presentations about DART:

Presentations about DART

Related Links

DART Contact list

PROGRAM dart_to_gitm

NAMELIST

MODULES USED

FILES Read

FILES Written

REFERENCES

ERROR CODES and CONDITIONS

KNOWN BUGS

FUTURE PLANS

Terms of Use

PROGRAM gitm_to_dart

NAMELIST

MODULES USED

FILES Read

FILES Written

REFERENCES

ERROR CODES and CONDITIONS

KNOWN BUGS

FUTURE PLANS

Terms of Use

Overview

NAMELIST

Grid information

model_mod variable storage

model_mod variable storage

The DART interface for MPAS (atm)

Compilation

Conversions

Converting between DART files and MPAS analysis files

NAMELIST

Example

REFERENCES

Document conventions

Overview of DART

Requirements: an F90 Compiler

Requirements: the netCDF library

Requirements: the udunits library

Unpacking the distribution.

Customizing the build scripts -- Overview.

Customizing the 'mkmf.template' file

FFLAGS

LIBS

Customizing the 'path_name' file

Building the Lorenz_63 DART project.

Running Lorenz_63.

Experiment Overview

1. Integrate the L63 model for a 'long' time.

2. Generate a set of ensemble initial conditions.

3. Simulate a particular observing system.

Non-backwards Compatible Changes

Requirements: an F90 Compiler

Matlab® Diagnostics